by Olena

Chocolate Coconut Flour Muffins

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Olena Osipov
5 from 5 votes

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

I love to use alternative ingredients in my muffins – like these almond flour banana muffins, chocolate quinoa muffins, and lemon zucchini muffins!

Cherry & Chocolate Coconut Flour Muffins

Remember coconut flour banana bread and 9 lbs of coconut flour? You would think the situation would be getting better and every month I would be using more and more of it slowly diminishing my coconut flour barrel. That is not the case. More than that, I am now a hoarder of 13 lbs of coconut flour. Hence, chocolate coconut flour muffins.

There are 2 underlying reasons why:

  1. My neighbour gave me her bag of Costco’s coconut flour. She had no idea what to do with it and was going to throw out. I can’t let that happen.
  2. I use only 1/2 – 1 cup per recipe because it is extremely moisture absorbing.

Unlike almond flour, which creates super moist baked goods (like almond flour brownies, waffles, and cakes like this chocolate cake and gluten free carrot cake) – coconut flour is actually 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.

Cherry & Chocolate Coconut Flour Muffins in muffin tins by the window

Many more years of coconut flour baking ahead for me. But that is OK because I have about 50 cups of frozen applesauce from my backyard that have to be used before new harvest this Fall. The key is to double or triple recipes at a time, I think. Less cleaning and more food.

On Tuesday, I made these chocolate coconut flour muffins and spaghetti squash quiche. It was rainy – a perfect day for baking. Dripping quiche all over the oven made my smoke alarm go off. I opened the window which was a perfect cooling muffin spot. A tip if you are impatient.

Bamboo Fiber Serve Bowl

My 9 year old got home from school and ate 3 muffins! they reminded him of my healthy chocolate muffins that are similarly fudgy. I always buy bags of frozen organic dark sweet cherries at Costco which kids polish off within a few weeks. They love to snack on frozen fruit in little ramekins. So, I thought these muffins would be a hit since they contain chocolate and cherries. AND I can hide anything behind those ingredients. Coconut flour, here you come.

In fact, I love hiding (and not hiding) nutritious ingredients in baked goods so that my children get in even more nutrients. Like these chocolate quinoa muffins, banana zucchini muffins, and almond muffins with lots of berries (not hidden!).

I bought this bowl at Homesense and love it. It was like $8, made out of organic bamboo fiber, super light and top rack dishwasher safe. And that grey colour. I do not use plastic so this was just perfect. Just sharing my hacks.

Coconut Flour and Cacao powder mixed in bowl

To be honest, I love coconut flour for its sweetness, high fiber and protein content comparable to chocolate quinoa muffins. It is really good for us. It is lighter than whole wheat flour. You just have to get used working with it.

Instead of traditional cocoa powder I am using cacao powder. 2 different things and you can use any but once you run out of cocoa powder, buy yourself organic fair trade cacao powder. Not only you will be consuming more antioxidants and less processed ingredient, but also eat ethically raised product where people and resources are treated fairly!

Malnourished children working to satisfy bursting at seams Westerners who LOVE their chocolate. Western world’s high demand => companies like Nestle putting pressure on cocoa bean manufacturers => child slavery => 1 in 7 obesity rate in the world => cancer. This world is so screwed up! A reason I do not buy Girl Scout cookies knocking on my door every week. Not that I am mean or think little girls are not important. My money is just better off tackling more important issues our world is facing today rather than supporting junk food production and kids’ slavery.

Frozen cherries and chocolate chips on top of batter


I added frozen cherries. No need to thaw. Cherry season is in a few months so you definitely can use fresh ones. A few readers have reported using dried cherries successfully. Probably around half amount of fresh. You will love these fudgy, sugar free and healthy chocolate coconut flour muffins!!! I tasted half of one and it was magnificent. Couldn’t eat more because goals, people, goals.

What are you up to this weekend? I will try to squeeze in a hike or a bike ride in between kids’ activities. I am a bit tired of all life centered around kids and house work. Man, where is my palapa on a beach?! A few more years and it will get better.

Have a super-duper weekend!

Other Healthy Chocolate Recipes

Chocolate Coconut Flour Muffins

Chocolate Coconut Flour Muffins

Cherry and Chocolate Coconut Flour Muffins - Moist, gluten and refined sugar free, healthy and tasty muffins recipe with fresh, frozen or dried cherries.
5 from 5 votes
Print Save Rate
Course: Breakfast or Snack
Cuisine: American
Prep Time: 5 minutes
Cook Time: 25 minutes
Total Time: 30 minutes
Servings: 12 muffins
Calories: 122kcal
Author: Olena Osipov



  • Preheat oven to 350 degrees F. Line muffin tin with liners** and spray with cooking spray.
  • 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 or freeze for up to 3 months.


    • *A few readers have reported using dried cherries successfully. Probably around half amount of fresh.
    • **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

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    43 comments on “Chocolate Coconut Flour Muffins

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    1. Hello,

      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. Thank you Olena for your quick reply! My husband and I love the oil free and sugar free muffin recipe. 😋

    2. 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 🙂

    3. 5 stars
      I substitued 2 bananas for the applesauce and it worked perfectly. My picky eaters ate it up no problem!

    4. 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!

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

    6. Hello,

      I am going to try this today but don’t have applesauce ?.
      In one of your blogs someone asked what to replace applesauce with and you replied by saying yogurt.
      However below you also say not to use yogurt:
      You have to use applesauce and not yogurt. That’s why your consistency is off. You can add a bit more flour and whisk it until no lumps.

      Is it possible to tell me what I should do?
      Thank you

      1. Coconut flour is more finicky than others. In this recipe, applesauce would be the best option. With baking, it is best to follow the recipe as closely as possible.

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