Healthy Muffin Recipes: One Base Batter, Six Ways

By Lee Funke

1/21/2026

I’ve always got muffins on my counter or tucked into the freezer because they’re one of those easy, grab-and-go snacks everyone in my house is happy to eat. Whether it’s breakfast, snack time, or something in between, muffins are usually my answer.

These healthy muffins are my go-to because they’re simple, made with everyday ingredients, and come together in under 40 minutes from start to finish. I make the base with whole grains and better-for-you ingredients, but the muffins still bake up soft, fluffy, and dessert-level good.

And the best part? That easy base recipe can turn into 6 different muffin flavors, and I’m sharing them all here.

Muffin Variations

Are muffins healthy? They can be! It really depends on how you make them. For those on specific meal plans, you can even make protein-rich muffins like my Chocolate Kodiak Protein Muffins . The 6 types of muffins in this post all start with the same wholesome base batter, which I then customize based on whatever I’m craving or what I have on hand.

If you’re ready to taste-test, here are the 6 flavors:

• Healthy Banana Nut Muffins
• Healthy Chocolate Muffins
• Cranberry Orange Muffins
• Apple Cinnamon Muffins
• Chocolate Pumpkin Zucchini Muffins
• Healthy Chocolate Chip Pumpkin Muffins

I use simple, better-for-you ingredients for the base that I’ve tested over and over so the muffins come out soft, fluffy, and reliably delicious every time.

Dry Ingredients :

White whole wheat flour : I love using King Arthur brand for light, fluffy muffins.

Coconut sugar: Light brown sugar works as a 1:1 substitute if needed.

Baking soda : Baking soda (not baking powder!) helps the muffins rise beautifully.

Salt: This one enhances the add-in flavors.

Wet Ingredients (same for all flavors, plus the pureed fruit):

Eggs: Eggs bind the muffins and contribute to fluffiness. I haven’t tested these with flax eggs, but if you do, let me know!

Maple syrup: This is the second sweetener used in these muffins. It’s a warm flavor and refined sugar-free.

Unsweetened almond milk: Any milk works here. Try cow’s milk or other dairy-free options like soy milk or coconut milk.

Melted coconut oil : Make sure to measure your coconut oil from the melted state for an accurate measurement.

Pureed fruit: This is the secret to moist, flavorful muffins!

Healthy Banana Nut Muffins

These banana muffins are made with mashed bananas, walnuts, ground cinnamon, and vanilla extract, making them slightly spicy and a great option for healthy breakfast muffins. If you prefer other nuts, like pecans, go for it!

• 1 cup mashed bananas
• 1/2 cup walnuts, chopped
• 1 teaspoon ground cinnamon
• 1 teaspoon vanilla extract

Healthy Chocolate Muffins

These are for the chocolate lovers out there. My healthy chocolate chip muffins are sweetened with mashed banana, chocolate chips, and cocoa powder, making them extra chocolatey.

• 1 cup mashed bananas
• 1/2 cup unsweetened cocoa powder
• 1/2 cup chocolate chips
• 1 teaspoon vanilla extract
• 1/4 cup almond milk (in addition to base recipe)

Cranberry Orange Muffins

This is the muffin I make when I want something fresh and not too sweet. The orange flavor is bright without being overpowering, and the cranberries add just the right pop. The whole-grain base makes them taste like a feel-good bake.

• 1 cup applesauce
• 1/2 teaspoon orange extract
• 1 tablespoon orange zest
• 2/3 cup dried cranberries

Apple Cinnamon Muffins

There’s nothing better than a warm, moist apple cinnamon muffin fresh from the oven. For these, I use applesauce, shredded apples, ground cinnamon, and a splash of vanilla extract.

• 1 cup applesauce
• 1 cup shredded apples (moisture removed)
• 2 teaspoons ground cinnamon
• 1 teaspoon vanilla extract

Chocolate Pumpkin Zucchini Muffins

I love a classic zucchini muffin , and adding pumpkin makes this version even better. Together, they create a super-moist, chocolatey muffin that tastes indulgent but includes 2 servings of veggies.

• 1 cup pumpkin puree
• 1/2 cup cocoa powder
• 1 cup shredded zucchini (moisture removed)
• 1/4 cup almond milk, unsweetened (in addition to base recipe)

Healthy Chocolate Chip Pumpkin Muffins

What’s better than pumpkin muffins ? Chocolate chip pumpkin muffins! They bake up super moist, with just a hint of cinnamon and melty chocolate chips in every bite.

• 1 cup pumpkin puree
• 1 teaspoon vanilla extract
• 1 teaspoon ground cinnamon
• 1/2 cup chocolate chips

Tips for Baking the Best Muffins

A few small baking tips can make the difference between dry, dense muffins and soft, fluffy ones. These simple tricks help the muffins bake evenly, stay moist, and turn out perfectly every time:

• Choose a mild oil. I prefer coconut oil because it’s light, doesn’t overpower the flavors, and keeps the texture soft and fluffy. Butter, olive oil, or vegetable oil can also work. Love coconut oil? Try my Coconut Oil Gingerbread Muffins next.

• Stick with white whole wheat flour . If you need to substitute flour, I suggest all-purpose flour, whole wheat flour, or an all-purpose gluten-free flour blend at a 1:1 ratio. I don’t recommend almond flour, oat flour, or coconut flour.

• Don’t overmix the batter. I mix just until the flour disappears. Overmixing develops the gluten too much and leads to dense or rubbery muffins instead of soft, fluffy ones.

• Use pureed fruit for moisture. Pureed fruits like bananas, applesauce, or pumpkin add natural sweetness and keeps the muffins extra moist without making them heavy.

• Watch your bake time. Overbaking is one of the fastest ways to dry out muffins. I start checking them early and pull them as soon as the centers are just set.

For muffins featuring rolled oats, try my Classic Oatmeal Muffins or my Blueberry Oatmeal Muffins !

Storage & Freezing

To store these muffins, let them cool completely, then transfer to an airtight container. Keep them in a cool, dark place for up to 3 days or in the fridge for 3-5 days. Since they include pureed fruit and real ingredients, they are more apt to mold quicker on the counter.

To freeze them, let muffins cool completely at room temperature, then transfer them to an airtight container or gallon-size plastic bag. (That’s what I prefer to do.) Remove as much air as possible and seal, and freeze for up to 3 months.

Ingredients1x2x3x

Base Dry Ingredients

• ▢ 1.5 cups white whole wheat flour
• ▢ ½ cup coconut sugar , or light brown sugar
• ▢ 1 teaspoon baking soda
• ▢ ⅛ teaspoon salt

Base Wet Ingredients

• ▢ 2 large eggs
• ▢ ½ cup maple syrup
• ▢ ½ cup unsweetened almond milk
• ▢ 3 tablespoons melted coconut oil
• ▢ 1 cup pureed fruit*

Instructions

• Preheat oven to 350ºF and line a muffin tin with muffin liners. I also suggest spraying your muffin liners with cooking spray, just in case.
• Place dry ingredients into a medium bowl and mix.
• In a large bowl, crack 2 eggs and whisk.
• Add maple syrup, almond milk, and preferred pureed fruit* and mix again.
• Add dry ingredients to wet ingredients and then mix. Then, add in melted coconut oil and mix again.
• Add any of the add-ins for one of the 6 muffin recipes in this post and mix again.
• Fill muffin cups about 3/4 of the way full. (These are going to be big muffins!) Place in the oven at 350ºF and bake for 18-22 minutes or until the center is fully cooked.
• Let cool for 5 minutes, and then remove from the muffin pan to continue cooling.

Tips & Notes

Watch It

Nutrition

Nutrition information is automatically calculated, so should only be used as an approximation.

Don’t forget to tag your posts on social media with the hashtag #fitfoodiefinds , we’d love to see what you’re up to!

What are healthy alternatives to sugar in muffins?

When baking muffins, I like to use sweeteners that add flavor and moisture without making them overly sweet. Coconut sugar is my go-to because it’s less refined and has a subtle caramel flavor. Light brown sugar works as a 1:1 swap if that’s what you have on hand.

I also rely on healthy ingredients like maple syrup or honey, both natural sweeteners that pair especially well with fruit-based muffins. Agave nectar could work, too, but I haven’t taste-tested that one.

Can you substitute applesauce for oil in muffins?

You can sometimes swap applesauce for oil in muffins and quick breads to make them a bit lighter, but I’d still only recommend a partial swap. Oil contributes to the tender, soft texture of muffins. Using 100% applesauce can make muffins denser or even a little rubbery, especially in recipes that rely on oil for lift and tenderness.

How long do healthy muffins last?

The healthy muffins in this recipe will keep for up to 3 days in a cool, dark place or up to 5 days in the fridge. I’d highly recommend the fridge, especially for any baked goods that include fresh or pureed fruit.

Healthy Muffins Base Recipe

Ingredients

Base Dry Ingredients

• 1.5 cups white whole wheat flour
• ½ cup coconut sugar or light brown sugar
• 1 teaspoon baking soda
• ⅛ teaspoon salt

Base Wet Ingredients

• 2 large eggs
• ½ cup maple syrup
• ½ cup unsweetened almond milk
• 3 tablespoons melted coconut oil
• 1 cup pureed fruit*

Instructions

• Preheat oven to 350ºF and line a muffin tin with muffin liners. I also suggest spraying your muffin liners with cooking spray, just in case.
• Place dry ingredients into a medium bowl and mix.
• In a large bowl, crack 2 eggs and whisk.
• Add maple syrup, almond milk, and preferred pureed fruit* and mix again.
• Add dry ingredients to wet ingredients and then mix. Then, add in melted coconut oil and mix again.
• Add any of the add-ins for one of the 6 muffin recipes in this post and mix again.
• Fill muffin cups about 3/4 of the way full. (These are going to be big muffins!) Place in the oven at 350ºF and bake for 18-22 minutes or until the center is fully cooked.
• Let cool for 5 minutes, and then remove from the muffin pan to continue cooling.

Video

Notes

Nutrition

Healthy Muffin Recipes: One Base Batter, Six Ways

By Lee Funke

1/21/2026

I’ve always got muffins on my counter or tucked into the freezer because they’re one of those easy, grab-and-go snacks everyone in my house is happy to eat. Whether it’s breakfast, snack time, or something in between, muffins are usually my answer.

These healthy muffins are my go-to because they’re simple, made with everyday ingredients, and come together in under 40 minutes from start to finish. I make the base with whole grains and better-for-you ingredients, but the muffins still bake up soft, fluffy, and dessert-level good.

And the best part? That easy base recipe can turn into 6 different muffin flavors, and I’m sharing them all here.

Muffin Variations

Are muffins healthy? They can be! It really depends on how you make them. For those on specific meal plans, you can even make protein-rich muffins like my Chocolate Kodiak Protein Muffins . The 6 types of muffins in this post all start with the same wholesome base batter, which I then customize based on whatever I’m craving or what I have on hand.

If you’re ready to taste-test, here are the 6 flavors:

• Healthy Banana Nut Muffins
• Healthy Chocolate Muffins
• Cranberry Orange Muffins
• Apple Cinnamon Muffins
• Chocolate Pumpkin Zucchini Muffins
• Healthy Chocolate Chip Pumpkin Muffins

I use simple, better-for-you ingredients for the base that I’ve tested over and over so the muffins come out soft, fluffy, and reliably delicious every time.

Dry Ingredients :

White whole wheat flour : I love using King Arthur brand for light, fluffy muffins.

Coconut sugar: Light brown sugar works as a 1:1 substitute if needed.

Baking soda : Baking soda (not baking powder!) helps the muffins rise beautifully.

Salt: This one enhances the add-in flavors.

Wet Ingredients (same for all flavors, plus the pureed fruit):

Eggs: Eggs bind the muffins and contribute to fluffiness. I haven’t tested these with flax eggs, but if you do, let me know!

Maple syrup: This is the second sweetener used in these muffins. It’s a warm flavor and refined sugar-free.

Unsweetened almond milk: Any milk works here. Try cow’s milk or other dairy-free options like soy milk or coconut milk.

Melted coconut oil : Make sure to measure your coconut oil from the melted state for an accurate measurement.

Pureed fruit: This is the secret to moist, flavorful muffins!

Healthy Banana Nut Muffins

These banana muffins are made with mashed bananas, walnuts, ground cinnamon, and vanilla extract, making them slightly spicy and a great option for healthy breakfast muffins. If you prefer other nuts, like pecans, go for it!

• 1 cup mashed bananas
• 1/2 cup walnuts, chopped
• 1 teaspoon ground cinnamon
• 1 teaspoon vanilla extract

Healthy Chocolate Muffins

These are for the chocolate lovers out there. My healthy chocolate chip muffins are sweetened with mashed banana, chocolate chips, and cocoa powder, making them extra chocolatey.

• 1 cup mashed bananas
• 1/2 cup unsweetened cocoa powder
• 1/2 cup chocolate chips
• 1 teaspoon vanilla extract
• 1/4 cup almond milk (in addition to base recipe)

Cranberry Orange Muffins

This is the muffin I make when I want something fresh and not too sweet. The orange flavor is bright without being overpowering, and the cranberries add just the right pop. The whole-grain base makes them taste like a feel-good bake.

• 1 cup applesauce
• 1/2 teaspoon orange extract
• 1 tablespoon orange zest
• 2/3 cup dried cranberries

Apple Cinnamon Muffins

There’s nothing better than a warm, moist apple cinnamon muffin fresh from the oven. For these, I use applesauce, shredded apples, ground cinnamon, and a splash of vanilla extract.

• 1 cup applesauce
• 1 cup shredded apples (moisture removed)
• 2 teaspoons ground cinnamon
• 1 teaspoon vanilla extract

Chocolate Pumpkin Zucchini Muffins

I love a classic zucchini muffin , and adding pumpkin makes this version even better. Together, they create a super-moist, chocolatey muffin that tastes indulgent but includes 2 servings of veggies.

• 1 cup pumpkin puree
• 1/2 cup cocoa powder
• 1 cup shredded zucchini (moisture removed)
• 1/4 cup almond milk, unsweetened (in addition to base recipe)

Healthy Chocolate Chip Pumpkin Muffins

What’s better than pumpkin muffins ? Chocolate chip pumpkin muffins! They bake up super moist, with just a hint of cinnamon and melty chocolate chips in every bite.

• 1 cup pumpkin puree
• 1 teaspoon vanilla extract
• 1 teaspoon ground cinnamon
• 1/2 cup chocolate chips

Tips for Baking the Best Muffins

A few small baking tips can make the difference between dry, dense muffins and soft, fluffy ones. These simple tricks help the muffins bake evenly, stay moist, and turn out perfectly every time:

• Choose a mild oil. I prefer coconut oil because it’s light, doesn’t overpower the flavors, and keeps the texture soft and fluffy. Butter, olive oil, or vegetable oil can also work. Love coconut oil? Try my Coconut Oil Gingerbread Muffins next.

• Stick with white whole wheat flour . If you need to substitute flour, I suggest all-purpose flour, whole wheat flour, or an all-purpose gluten-free flour blend at a 1:1 ratio. I don’t recommend almond flour, oat flour, or coconut flour.

• Don’t overmix the batter. I mix just until the flour disappears. Overmixing develops the gluten too much and leads to dense or rubbery muffins instead of soft, fluffy ones.

• Use pureed fruit for moisture. Pureed fruits like bananas, applesauce, or pumpkin add natural sweetness and keeps the muffins extra moist without making them heavy.

• Watch your bake time. Overbaking is one of the fastest ways to dry out muffins. I start checking them early and pull them as soon as the centers are just set.

For muffins featuring rolled oats, try my Classic Oatmeal Muffins or my Blueberry Oatmeal Muffins !

Storage & Freezing

To store these muffins, let them cool completely, then transfer to an airtight container. Keep them in a cool, dark place for up to 3 days or in the fridge for 3-5 days. Since they include pureed fruit and real ingredients, they are more apt to mold quicker on the counter.

To freeze them, let muffins cool completely at room temperature, then transfer them to an airtight container or gallon-size plastic bag. (That’s what I prefer to do.) Remove as much air as possible and seal, and freeze for up to 3 months.

Ingredients1x2x3x

Base Dry Ingredients

• ▢ 1.5 cups white whole wheat flour
• ▢ ½ cup coconut sugar , or light brown sugar
• ▢ 1 teaspoon baking soda
• ▢ ⅛ teaspoon salt

Base Wet Ingredients

• ▢ 2 large eggs
• ▢ ½ cup maple syrup
• ▢ ½ cup unsweetened almond milk
• ▢ 3 tablespoons melted coconut oil
• ▢ 1 cup pureed fruit*

Instructions

• Preheat oven to 350ºF and line a muffin tin with muffin liners. I also suggest spraying your muffin liners with cooking spray, just in case.
• Place dry ingredients into a medium bowl and mix.
• In a large bowl, crack 2 eggs and whisk.
• Add maple syrup, almond milk, and preferred pureed fruit* and mix again.
• Add dry ingredients to wet ingredients and then mix. Then, add in melted coconut oil and mix again.
• Add any of the add-ins for one of the 6 muffin recipes in this post and mix again.
• Fill muffin cups about 3/4 of the way full. (These are going to be big muffins!) Place in the oven at 350ºF and bake for 18-22 minutes or until the center is fully cooked.
• Let cool for 5 minutes, and then remove from the muffin pan to continue cooling.

Tips & Notes

Watch It

Nutrition

Nutrition information is automatically calculated, so should only be used as an approximation.

Don’t forget to tag your posts on social media with the hashtag #fitfoodiefinds , we’d love to see what you’re up to!

What are healthy alternatives to sugar in muffins?

When baking muffins, I like to use sweeteners that add flavor and moisture without making them overly sweet. Coconut sugar is my go-to because it’s less refined and has a subtle caramel flavor. Light brown sugar works as a 1:1 swap if that’s what you have on hand.

I also rely on healthy ingredients like maple syrup or honey, both natural sweeteners that pair especially well with fruit-based muffins. Agave nectar could work, too, but I haven’t taste-tested that one.

Can you substitute applesauce for oil in muffins?

You can sometimes swap applesauce for oil in muffins and quick breads to make them a bit lighter, but I’d still only recommend a partial swap. Oil contributes to the tender, soft texture of muffins. Using 100% applesauce can make muffins denser or even a little rubbery, especially in recipes that rely on oil for lift and tenderness.

How long do healthy muffins last?

The healthy muffins in this recipe will keep for up to 3 days in a cool, dark place or up to 5 days in the fridge. I’d highly recommend the fridge, especially for any baked goods that include fresh or pureed fruit.

Healthy Muffin Recipes: One Base Batter, Six Ways

By Lee Funke

1/21/2026

I’ve always got muffins on my counter or tucked into the freezer because they’re one of those easy, grab-and-go snacks everyone in my house is happy to eat. Whether it’s breakfast, snack time, or something in between, muffins are usually my answer.

These healthy muffins are my go-to because they’re simple, made with everyday ingredients, and come together in under 40 minutes from start to finish. I make the base with whole grains and better-for-you ingredients, but the muffins still bake up soft, fluffy, and dessert-level good.

And the best part? That easy base recipe can turn into 6 different muffin flavors, and I’m sharing them all here.

Muffin Variations

Are muffins healthy? They can be! It really depends on how you make them. For those on specific meal plans, you can even make protein-rich muffins like my Chocolate Kodiak Protein Muffins . The 6 types of muffins in this post all start with the same wholesome base batter, which I then customize based on whatever I’m craving or what I have on hand.

If you’re ready to taste-test, here are the 6 flavors:

• Healthy Banana Nut Muffins
• Healthy Chocolate Muffins
• Cranberry Orange Muffins
• Apple Cinnamon Muffins
• Chocolate Pumpkin Zucchini Muffins
• Healthy Chocolate Chip Pumpkin Muffins

I use simple, better-for-you ingredients for the base that I’ve tested over and over so the muffins come out soft, fluffy, and reliably delicious every time.

Dry Ingredients :

White whole wheat flour : I love using King Arthur brand for light, fluffy muffins.

Coconut sugar: Light brown sugar works as a 1:1 substitute if needed.

Baking soda : Baking soda (not baking powder!) helps the muffins rise beautifully.

Salt: This one enhances the add-in flavors.

Wet Ingredients (same for all flavors, plus the pureed fruit):

Eggs: Eggs bind the muffins and contribute to fluffiness. I haven’t tested these with flax eggs, but if you do, let me know!

Maple syrup: This is the second sweetener used in these muffins. It’s a warm flavor and refined sugar-free.

Unsweetened almond milk: Any milk works here. Try cow’s milk or other dairy-free options like soy milk or coconut milk.

Melted coconut oil : Make sure to measure your coconut oil from the melted state for an accurate measurement.

Pureed fruit: This is the secret to moist, flavorful muffins!

Healthy Banana Nut Muffins

These banana muffins are made with mashed bananas, walnuts, ground cinnamon, and vanilla extract, making them slightly spicy and a great option for healthy breakfast muffins. If you prefer other nuts, like pecans, go for it!

• 1 cup mashed bananas
• 1/2 cup walnuts, chopped
• 1 teaspoon ground cinnamon
• 1 teaspoon vanilla extract

Healthy Chocolate Muffins

These are for the chocolate lovers out there. My healthy chocolate chip muffins are sweetened with mashed banana, chocolate chips, and cocoa powder, making them extra chocolatey.

• 1 cup mashed bananas
• 1/2 cup unsweetened cocoa powder
• 1/2 cup chocolate chips
• 1 teaspoon vanilla extract
• 1/4 cup almond milk (in addition to base recipe)

Cranberry Orange Muffins

This is the muffin I make when I want something fresh and not too sweet. The orange flavor is bright without being overpowering, and the cranberries add just the right pop. The whole-grain base makes them taste like a feel-good bake.

• 1 cup applesauce
• 1/2 teaspoon orange extract
• 1 tablespoon orange zest
• 2/3 cup dried cranberries

Apple Cinnamon Muffins

There’s nothing better than a warm, moist apple cinnamon muffin fresh from the oven. For these, I use applesauce, shredded apples, ground cinnamon, and a splash of vanilla extract.

• 1 cup applesauce
• 1 cup shredded apples (moisture removed)
• 2 teaspoons ground cinnamon
• 1 teaspoon vanilla extract

Chocolate Pumpkin Zucchini Muffins

I love a classic zucchini muffin , and adding pumpkin makes this version even better. Together, they create a super-moist, chocolatey muffin that tastes indulgent but includes 2 servings of veggies.

• 1 cup pumpkin puree
• 1/2 cup cocoa powder
• 1 cup shredded zucchini (moisture removed)
• 1/4 cup almond milk, unsweetened (in addition to base recipe)

Healthy Chocolate Chip Pumpkin Muffins

What’s better than pumpkin muffins ? Chocolate chip pumpkin muffins! They bake up super moist, with just a hint of cinnamon and melty chocolate chips in every bite.

• 1 cup pumpkin puree
• 1 teaspoon vanilla extract
• 1 teaspoon ground cinnamon
• 1/2 cup chocolate chips

Tips for Baking the Best Muffins

A few small baking tips can make the difference between dry, dense muffins and soft, fluffy ones. These simple tricks help the muffins bake evenly, stay moist, and turn out perfectly every time:

• Choose a mild oil. I prefer coconut oil because it’s light, doesn’t overpower the flavors, and keeps the texture soft and fluffy. Butter, olive oil, or vegetable oil can also work. Love coconut oil? Try my Coconut Oil Gingerbread Muffins next.

• Stick with white whole wheat flour . If you need to substitute flour, I suggest all-purpose flour, whole wheat flour, or an all-purpose gluten-free flour blend at a 1:1 ratio. I don’t recommend almond flour, oat flour, or coconut flour.

• Don’t overmix the batter. I mix just until the flour disappears. Overmixing develops the gluten too much and leads to dense or rubbery muffins instead of soft, fluffy ones.

• Use pureed fruit for moisture. Pureed fruits like bananas, applesauce, or pumpkin add natural sweetness and keeps the muffins extra moist without making them heavy.

• Watch your bake time. Overbaking is one of the fastest ways to dry out muffins. I start checking them early and pull them as soon as the centers are just set.

For muffins featuring rolled oats, try my Classic Oatmeal Muffins or my Blueberry Oatmeal Muffins !

Storage & Freezing

To store these muffins, let them cool completely, then transfer to an airtight container. Keep them in a cool, dark place for up to 3 days or in the fridge for 3-5 days. Since they include pureed fruit and real ingredients, they are more apt to mold quicker on the counter.

To freeze them, let muffins cool completely at room temperature, then transfer them to an airtight container or gallon-size plastic bag. (That’s what I prefer to do.) Remove as much air as possible and seal, and freeze for up to 3 months.

Ingredients1x2x3x

Base Dry Ingredients

• ▢ 1.5 cups white whole wheat flour
• ▢ ½ cup coconut sugar , or light brown sugar
• ▢ 1 teaspoon baking soda
• ▢ ⅛ teaspoon salt

Base Wet Ingredients

• ▢ 2 large eggs
• ▢ ½ cup maple syrup
• ▢ ½ cup unsweetened almond milk
• ▢ 3 tablespoons melted coconut oil
• ▢ 1 cup pureed fruit*

Instructions

• Preheat oven to 350ºF and line a muffin tin with muffin liners. I also suggest spraying your muffin liners with cooking spray, just in case.
• Place dry ingredients into a medium bowl and mix.
• In a large bowl, crack 2 eggs and whisk.
• Add maple syrup, almond milk, and preferred pureed fruit* and mix again.
• Add dry ingredients to wet ingredients and then mix. Then, add in melted coconut oil and mix again.
• Add any of the add-ins for one of the 6 muffin recipes in this post and mix again.
• Fill muffin cups about 3/4 of the way full. (These are going to be big muffins!) Place in the oven at 350ºF and bake for 18-22 minutes or until the center is fully cooked.
• Let cool for 5 minutes, and then remove from the muffin pan to continue cooling.

Tips & Notes

Watch It

Nutrition

Nutrition information is automatically calculated, so should only be used as an approximation.

Don’t forget to tag your posts on social media with the hashtag #fitfoodiefinds , we’d love to see what you’re up to!

What are healthy alternatives to sugar in muffins?

When baking muffins, I like to use sweeteners that add flavor and moisture without making them overly sweet. Coconut sugar is my go-to because it’s less refined and has a subtle caramel flavor. Light brown sugar works as a 1:1 swap if that’s what you have on hand.

I also rely on healthy ingredients like maple syrup or honey, both natural sweeteners that pair especially well with fruit-based muffins. Agave nectar could work, too, but I haven’t taste-tested that one.

Can you substitute applesauce for oil in muffins?

You can sometimes swap applesauce for oil in muffins and quick breads to make them a bit lighter, but I’d still only recommend a partial swap. Oil contributes to the tender, soft texture of muffins. Using 100% applesauce can make muffins denser or even a little rubbery, especially in recipes that rely on oil for lift and tenderness.

How long do healthy muffins last?

The healthy muffins in this recipe will keep for up to 3 days in a cool, dark place or up to 5 days in the fridge. I’d highly recommend the fridge, especially for any baked goods that include fresh or pureed fruit.

Healthy Muffin Recipes: One Base Batter, Six Ways

By Lee Funke

1/21/2026

I’ve always got muffins on my counter or tucked into the freezer because they’re one of those easy, grab-and-go snacks everyone in my house is happy to eat. Whether it’s breakfast, snack time, or something in between, muffins are usually my answer.

These healthy muffins are my go-to because they’re simple, made with everyday ingredients, and come together in under 40 minutes from start to finish. I make the base with whole grains and better-for-you ingredients, but the muffins still bake up soft, fluffy, and dessert-level good.

And the best part? That easy base recipe can turn into 6 different muffin flavors, and I’m sharing them all here.

Muffin Variations

Are muffins healthy? They can be! It really depends on how you make them. For those on specific meal plans, you can even make protein-rich muffins like my Chocolate Kodiak Protein Muffins . The 6 types of muffins in this post all start with the same wholesome base batter, which I then customize based on whatever I’m craving or what I have on hand.

If you’re ready to taste-test, here are the 6 flavors:

• Healthy Banana Nut Muffins
• Healthy Chocolate Muffins
• Cranberry Orange Muffins
• Apple Cinnamon Muffins
• Chocolate Pumpkin Zucchini Muffins
• Healthy Chocolate Chip Pumpkin Muffins

I use simple, better-for-you ingredients for the base that I’ve tested over and over so the muffins come out soft, fluffy, and reliably delicious every time.

Dry Ingredients :

White whole wheat flour : I love using King Arthur brand for light, fluffy muffins.

Coconut sugar: Light brown sugar works as a 1:1 substitute if needed.

Baking soda : Baking soda (not baking powder!) helps the muffins rise beautifully.

Salt: This one enhances the add-in flavors.

Wet Ingredients (same for all flavors, plus the pureed fruit):

Eggs: Eggs bind the muffins and contribute to fluffiness. I haven’t tested these with flax eggs, but if you do, let me know!

Maple syrup: This is the second sweetener used in these muffins. It’s a warm flavor and refined sugar-free.

Unsweetened almond milk: Any milk works here. Try cow’s milk or other dairy-free options like soy milk or coconut milk.

Melted coconut oil : Make sure to measure your coconut oil from the melted state for an accurate measurement.

Pureed fruit: This is the secret to moist, flavorful muffins!

Healthy Banana Nut Muffins

These banana muffins are made with mashed bananas, walnuts, ground cinnamon, and vanilla extract, making them slightly spicy and a great option for healthy breakfast muffins. If you prefer other nuts, like pecans, go for it!

• 1 cup mashed bananas
• 1/2 cup walnuts, chopped
• 1 teaspoon ground cinnamon
• 1 teaspoon vanilla extract

Healthy Chocolate Muffins

These are for the chocolate lovers out there. My healthy chocolate chip muffins are sweetened with mashed banana, chocolate chips, and cocoa powder, making them extra chocolatey.

• 1 cup mashed bananas
• 1/2 cup unsweetened cocoa powder
• 1/2 cup chocolate chips
• 1 teaspoon vanilla extract
• 1/4 cup almond milk (in addition to base recipe)

Cranberry Orange Muffins

This is the muffin I make when I want something fresh and not too sweet. The orange flavor is bright without being overpowering, and the cranberries add just the right pop. The whole-grain base makes them taste like a feel-good bake.

• 1 cup applesauce
• 1/2 teaspoon orange extract
• 1 tablespoon orange zest
• 2/3 cup dried cranberries

Apple Cinnamon Muffins

There’s nothing better than a warm, moist apple cinnamon muffin fresh from the oven. For these, I use applesauce, shredded apples, ground cinnamon, and a splash of vanilla extract.

• 1 cup applesauce
• 1 cup shredded apples (moisture removed)
• 2 teaspoons ground cinnamon
• 1 teaspoon vanilla extract

Chocolate Pumpkin Zucchini Muffins

I love a classic zucchini muffin , and adding pumpkin makes this version even better. Together, they create a super-moist, chocolatey muffin that tastes indulgent but includes 2 servings of veggies.

• 1 cup pumpkin puree
• 1/2 cup cocoa powder
• 1 cup shredded zucchini (moisture removed)
• 1/4 cup almond milk, unsweetened (in addition to base recipe)

Healthy Chocolate Chip Pumpkin Muffins

What’s better than pumpkin muffins ? Chocolate chip pumpkin muffins! They bake up super moist, with just a hint of cinnamon and melty chocolate chips in every bite.

• 1 cup pumpkin puree
• 1 teaspoon vanilla extract
• 1 teaspoon ground cinnamon
• 1/2 cup chocolate chips

Tips for Baking the Best Muffins

A few small baking tips can make the difference between dry, dense muffins and soft, fluffy ones. These simple tricks help the muffins bake evenly, stay moist, and turn out perfectly every time:

• Choose a mild oil. I prefer coconut oil because it’s light, doesn’t overpower the flavors, and keeps the texture soft and fluffy. Butter, olive oil, or vegetable oil can also work. Love coconut oil? Try my Coconut Oil Gingerbread Muffins next.

• Stick with white whole wheat flour . If you need to substitute flour, I suggest all-purpose flour, whole wheat flour, or an all-purpose gluten-free flour blend at a 1:1 ratio. I don’t recommend almond flour, oat flour, or coconut flour.

• Don’t overmix the batter. I mix just until the flour disappears. Overmixing develops the gluten too much and leads to dense or rubbery muffins instead of soft, fluffy ones.

• Use pureed fruit for moisture. Pureed fruits like bananas, applesauce, or pumpkin add natural sweetness and keeps the muffins extra moist without making them heavy.

• Watch your bake time. Overbaking is one of the fastest ways to dry out muffins. I start checking them early and pull them as soon as the centers are just set.

For muffins featuring rolled oats, try my Classic Oatmeal Muffins or my Blueberry Oatmeal Muffins !

Storage & Freezing

To store these muffins, let them cool completely, then transfer to an airtight container. Keep them in a cool, dark place for up to 3 days or in the fridge for 3-5 days. Since they include pureed fruit and real ingredients, they are more apt to mold quicker on the counter.

To freeze them, let muffins cool completely at room temperature, then transfer them to an airtight container or gallon-size plastic bag. (That’s what I prefer to do.) Remove as much air as possible and seal, and freeze for up to 3 months.

Ingredients1x2x3x

Base Dry Ingredients

• ▢ 1.5 cups white whole wheat flour
• ▢ ½ cup coconut sugar , or light brown sugar
• ▢ 1 teaspoon baking soda
• ▢ ⅛ teaspoon salt

Base Wet Ingredients

• ▢ 2 large eggs
• ▢ ½ cup maple syrup
• ▢ ½ cup unsweetened almond milk
• ▢ 3 tablespoons melted coconut oil
• ▢ 1 cup pureed fruit*

Instructions

• Preheat oven to 350ºF and line a muffin tin with muffin liners. I also suggest spraying your muffin liners with cooking spray, just in case.
• Place dry ingredients into a medium bowl and mix.
• In a large bowl, crack 2 eggs and whisk.
• Add maple syrup, almond milk, and preferred pureed fruit* and mix again.
• Add dry ingredients to wet ingredients and then mix. Then, add in melted coconut oil and mix again.
• Add any of the add-ins for one of the 6 muffin recipes in this post and mix again.
• Fill muffin cups about 3/4 of the way full. (These are going to be big muffins!) Place in the oven at 350ºF and bake for 18-22 minutes or until the center is fully cooked.
• Let cool for 5 minutes, and then remove from the muffin pan to continue cooling.

Tips & Notes

Watch It

Nutrition

Nutrition information is automatically calculated, so should only be used as an approximation.

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What are healthy alternatives to sugar in muffins?

When baking muffins, I like to use sweeteners that add flavor and moisture without making them overly sweet. Coconut sugar is my go-to because it’s less refined and has a subtle caramel flavor. Light brown sugar works as a 1:1 swap if that’s what you have on hand.

I also rely on healthy ingredients like maple syrup or honey, both natural sweeteners that pair especially well with fruit-based muffins. Agave nectar could work, too, but I haven’t taste-tested that one.

Can you substitute applesauce for oil in muffins?

You can sometimes swap applesauce for oil in muffins and quick breads to make them a bit lighter, but I’d still only recommend a partial swap. Oil contributes to the tender, soft texture of muffins. Using 100% applesauce can make muffins denser or even a little rubbery, especially in recipes that rely on oil for lift and tenderness.

How long do healthy muffins last?

The healthy muffins in this recipe will keep for up to 3 days in a cool, dark place or up to 5 days in the fridge. I’d highly recommend the fridge, especially for any baked goods that include fresh or pureed fruit.