These Chocolate Coconut Flour Muffins are dense, fudgy, and packed with chocolate and cherry flavor! Best of all they’re naturally gluten free and dairy free!

I love to use healthy alternative ingredients in my baking like this coconut flour banana bread!

Double chocolate coconut flour muffins with cherries and chocolate chips.

If you’re looking for a rich, indulgent, and deliciously fudgy chocolate-y muffin that just happens to be healthy, I am happy to help!

I’m sharing with you the best muffin recipe that caters to the chocolate lover in you and to those that are looking for healthy snack ideas!

They might remind you of my healthy chocolate muffins and healthy chocolate bread that are similarly fudgy.

These muffins are super moist, flavorful and can be kept frozen for months, so I suggest doubling the batch.

Unlike almond flour, which creates super moist baked goods like almond flour banana muffins, coconut flour is very absorbent. For this reason, learning to bake with it can be tricky and it definitely shouldn’t be used to substitute other flours without other ingredient tweaks.

Ingredients You’ll Need

Coconut flour, milk, applesauce, eggs, chocolate chips, cherries, cacao powder, maple syrup, coconut oil, vanilla, cinnamon, baking powder, baking soda, cooking spray, salt.

The list may look long, but every ingredient plays an important role when baking with coconut flour. If necessary, see below for some ingredient substitutions.

  • Large eggs: When using gluten free flour, especially, it’s important to use eggs for binding. They will also help to add moisture, which coconut flour doesn’t provide.
  • Applesauce: Replaces the oil or butter in baking which allows us to use less fat even if we still do use either one. Can also use yogurt or mashed bananas.
  • Milk: You can use whatever milk you have on hand. I usually have unsweetened almond milk.
  • Maple syrup: Use any liquid sweetener you want, including any sugar free substitutes. Just as long as you’re not altering the wet to dry ingredient ratio.
  • Coconut oil: Can use melted butter or any mild tasting oil instead.
  • Pure vanilla extract: A flavor enhancer!
  • Cacao powder: Not to be confused with cocoa powder. Cacao powder is made from unroasted beans which means it is slightly less processed than cocoa powder. Either can be used.
  • Baking soda & baking powder: Leavening agents that will work hard to get your muffins to a light and fluffy texture.
  • Cinnamon: Just another layer of flavor that pairs well with chocolate.
  • Coconut flour: Absorbs liquid easily, so follow directions carefully!
  • Dark chocolate chips: The second type of chocolate in these muffins.
  • Cherries: Fresh or frozen pitted cherries.
  • Cooking spray: Don’t skip this! You’ll need to make sure your muffins don’t stick to the tin once baked.

How to Make Chocolate Coconut Flour Muffins

This is a one bowl recipe that produces warm chocolate-y muffins in 30 minutes, so even if you don’t have some frozen on hand, they’re just as easy to whip up in a hurry!

Coconut flour and cacao powder mixed in bowl with a whisk.

First, you’ll grab a medium bowl and mix the wet ingredients, followed by all of the dry ingredients except the flour.

Then, you’ll add the coconut flour to the batter and stir it well. Toss in the cherries and chocolate chips and fold in to combine and voila!

Divide the batter into the tin and bake for 25 minutes. Don’t forget to allow them to cool first!


Frozen cherries and chocolate chips on top of batter in bowl.


Here’s a list of a few easy swaps:

  • Dried cherries. A few readers have reported using dried cherries successfully. If you try this, you’ll probably need around half the amount of fresh cherries.
  • A different extract. Swap out the vanilla extract for almond extract instead. Consider using a little less to ensure it doesn’t overpower the taste.
  • Milk. As mentioned above, use any milk. Coconut milk might be a nice way to play up the coconut flavor. The higher fat content will lead to richer textures.
  • Dark chocolate bar chopped instead of chocolate chips can work. If you’re OK with the slightly bitter flavor, you could also use cacao nibs.

Expert Tips and FAQs

  • Use paper liners. Baked goods using coconut flour tend to be delicate. Muffin liners will help keep them together.
  • Ice cream scoop. Divide the batter evenly by using an ice cream scoop. This helps to make sure each one is the same size, for even baking.
Can I substitute coconut flour?


Can I use an egg replacer?

No. I don’t recommend it. Not only are we using eggs in this recipe but we’re using 3 large ones! They are needed for structure when using coconut flour.

What can I use instead of cherries?

Any fresh or frozen berries will work. Think blueberries, raspberries, blackberries etc. Also dried fruit is OK but use half amount.

What is the best way to enjoy these muffins?

They work as a breakfast, snack, or even dessert! Slice it in half and spread some nut butter or butter on each half. You could dust it with a little powdered sugar for a treat. If you want to get ridiculous, top it with a dollop of healthy chocolate frosting!

Storing Leftovers

These don’t need to be kept in the fridge, just a spot on the counter will do. Enjoy them for a few days.

If you’ve made a double batch or want to freeze what hasn’t been eaten, you can store them in the freezer for up to 3 months in an airtight container. Then, when you’re ready to take one or two out, allow them to thaw overnight. Enjoy them at room temperature or warmed up a bit!

Storage Tip

For more best practices on storing leftover muffins, check out my guides how to store muffins and how to freeze muffins.

More Healthy Chocolate Recipes

Chocolate coconut flour muffins in muffin tin by the window.
Double chocolate coconut flour muffins with cherries and chocolate chips.

Double Chocolate Coconut Flour Muffins

These Chocolate Coconut Flour Muffins are dense, fudgy, and packed with chocolate and cherry flavor!
5 from 23 votes
Servings 12 muffins
Calories 122
Diet Gluten Free
Prep Time 5 minutes
Cook Time 25 minutes
Cooling Time 30 minutes
Total Time 1 hour



  • Preheat oven to 350 degrees F. Line muffin tin with liners and spray with cooking spray. Set aside.
  • In a large mixing bowl, whisk the eggs. Add applesauce, milk, maple syrup, coconut oil, vanilla and whisk well to combine. Add cacao powder, baking soda, baking powder, cinnamon and whisk until combined.
  • Add coconut flour and stir well. Add chocolate chips and cherries; give a few gentle stirs to incorporate.
  • Using large ice cream scoop, divide batter between 12 openings. Bake for 25 minutes or until toothpick inserted in the middle comes out sort of clean.
  • Remove from the oven and let cool for 10-15 minutes. Transfer to a cooling rack and let muffins cool off another 15 minutes to firm up.


  • Store: Store in a cool dry place for up to 3 – 4 days
  • Freeze: Airtight container up to 3 months.
  • Cherries: A few readers have reported using dried cherries successfully. Probably around half amount of fresh.
  • Liners: I highly recommend to use liners as coconut flour muffins are delicate.


Serving: 1muffin | Calories: 122kcal | Carbohydrates: 17g | Protein: 3g | Fat: 6g | Saturated Fat: 4g | Cholesterol: 41mg | Sodium: 190mg | Fiber: 3g | Sugar: 11g
Course: Breakfast or Snack
Cuisine: North American
Author: Olena Osipov
Did you make this recipe?Mention @ifoodreal or tag #ifoodreal!

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About Olena

Welcome! I grew up in Ukraine watching my grandma cook with simple ingredients. I have spent the last 11 years making it my mission to help you cook quick and easy meals for your family!

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  1. 5 stars
    This recipe looks fabulous Olena! I love baking with coconut flour and just made your coconut flour banana bread, it was amazing! Can’t wait to try these!
    Question: Can I omit the cherries or sub strawberries instead?

    1. So happy to hear coconut flour banana bread worked! Yes, sure, omit the cherries or use strawberries. Strawberries might make muffins a bit wet though, toss with 1 tablespoon of cornstarch in a separate bowl before adding. Also use fresh strawberries, not frozen, because they leak a lot more and are not sweet.

  2. 5 stars

    Thank you for sharing your recipes. They are easy to make and tastes great. With this particular receipt, I am not able to find fresh, dried or frozen cherries in my country. Are there any other berrries that I can use as a replacement? I am able to find the canned ones soak in syrup. Can I use these?

    1. Hi Daisy. You are so welcome! You can use dried cranberries or apricots, chopped. Yes, canned cherries rae OK if you drain them well. Enjoy!!!

      1. 5 stars
        Thank you Olena for your quick reply! My husband and I love the oil free and sugar free muffin recipe. πŸ˜‹

  3. 5 stars
    Thank you Olena for the recipe! I love it love it love it and everyone who have tried the muffins loved it too! I have substituted 1/2 cup mashed banana for the applesauce and also about 1/2 cup yogurt for the applesauce and both worked too! Reason because I don’t have any applesauce and I’m not fussed about it. Yogurt turned out nicer, fuller compared to banana because it has a higher sugar content but the banana ones were also packed with flavours! I cannot stop making these now πŸ™‚

  4. 5 stars
    I substitued 2 bananas for the applesauce and it worked perfectly. My picky eaters ate it up no problem!

  5. 5 stars
    I made a batch of these muffins this morning. To be honest, I was a bit skeptical about baking with coconut flour. The liquid to dry ratios is something I just cannot seem to get right for some reason. But these, OMG, THESE were fantastic! Hands down one of the best muffins I’ve ever eaten! So soft and moist they’re more like cupcakes! They were all gone by lunchtime. My 5 year old alone ate 4. Thanks so much Olena!
    I am looking forward, VERY MUCH, to a recipe developed by you for ‘healthy cornmeal orange muffins’ I love this flavor combination but most recipes I’ve seen use humongous amounts of butter and sugar. Also, they use the zest or juice only. I like to cook oranges(mandarines) in boiling water until soft, then take the peeps out, blitz them in the food processor and use that puree as I would applesauce or bananas. You think that’ll work for cornmeal muffins?
    Thanks again for all of your awesome recipes!

  6. 5 stars
    I loved these! They’re rich, full of flavor and I don’t find them gritty! I will be making these again.

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