These gluten-free coconut flour chocolate muffins are divine (but healthy!), and are made with coconut flour, coconut oil, and a hint of sweet bananas. Enjoy!

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close up shot of coconut flour chocolate muffin with chocolate chips on top, sitting on a parchment paper surface

These coconut flour muffins are super sneaky. They’re a banana-chocolate mashup, which is actually a delightful combination, but the script is flipped, and the chocolate takes the leading role, while the banana provides the support. They’re also totally healthy, which I’ll get to in a sec. They are sure to please any sweet tooth!

There are a few dream-team combos in the food world, many involving chocolate. I’ll tell you right now that chocolate and peanut butter are soulmates (try my homemade chocolate peanut butter cups and you’ll see), but I’ll tell you what: chocolate and banana are kindred spirits. The hint of sweet banana compliments the chocolate motif perfectly.

But seriously: don’t tell my kids these are healthy.

If they find out, I won’t be able to use them as the ultimate bribe. “If you finish your chores we call have cupcakes as a snack!” *wink*

It’s not just my kids, is it? Bribes (or, the more politically correct term these days: rewards) are the key to good parenting. I say that with a wink and a smile but guys – we all know it’s true. Our pre-kid parenting knowledge is eating some serious humble pie, amiright?!

Okay, okay, serious sidebar here. I joke, but for real – I do believe in being transparent and factual with your kids 97% of the time about what they’re eating. Otherwise, how will they realize that healthy food can actually taste amazing?! In the toddler and preschooler stage we use “creative framing” of foods (aka: calling them cupcakes) way more often, but when they get older we start to get more and more transparent and it’s really fun to watch them start to take agency over the types of foods they want to use to fuel their bodies.

Double Chocolate Coconut Flour Muffins FAQ

Are muffins with coconut flour healthy?

Yes! Even if you include grains in your diet, we can all benefit from some snack recipes that aren’t wheat-based. Also, more eggs = more protein. Also, these muffins are lightly sweetened with banana and a bit of honey. There are 12 grams of sugar per serving, but 6 grams of fiber which helps to mitigate the glucose response.

In contrast – most store-bought bakery muffins typically contain as much as 50-70g of sugar (processed), and they are mostly empty carbs that will give a huge glucose spike.

Following a dietary style? These sweet treats aren’t keto chocolate muffins because of the sugar from the bananas but they are paleo chocolate muffins. They are, of course, gluten-free, and also dairy-free.

Bottom line? They’re legit healthy! Check out some of the star ingredients in these healthy chocolate muffins.

Coconut flour. It is made from dried coconut meat. The coconut milk is removed, leaving the meat that once dried is ground into flour. It is loaded with protein and is a high fiber food. Some people with nut allergies can’t tolerate coconut, so please keep that in mind.
Eggs. They are an awesome protein and great food to always have on hand for quick meals.
Coconut oil. It is a superfood and full of healthy fats.
No refined sugar. Except for the dark chocolate chips, which are at a minimum and could technically be skipped, but life is short, guys. (If you want to use sugar-free chocolate chips, there a few great brands out there.)
Unsweetened cocoa powder. It is full of antioxidants and is naturally low carb, with only 3g net carbs per tablespoon.

These coconut flour healthy muffins with chocolate and bananas are some of our favorites as you can now see why. Everyone needs a sweet treat in their life that is good for them.

Overhead shot of a dozen coconut flour chocolate muffins on a black cooling rack and white surface,

How to make muffins with coconut flour?

Baking with coconut flour has a bit of a learning curve but it’s really easy. One of the first things you need to remember is that one cup of coconut flour does not equal one cup of regular flour or gluten-free flour blend. It’s more of a 1:4 ratio.

Coconut flour is a very “thirsty” flour that requires a lot of moisture, normally from a high amount of eggs. The nice thing is that they are not very crumbly like almond flour chocolate muffins might be.

One of the nice things is that the taste of coconut is not in your face. It’s subtle. The chocolate flavor shines in these tasty muffins. Also, some people (me!) aren’t always a fan of baked goods with coconut flour since they can sometimes taste a bit eggy or spongy. The banana in this recipe interrupts that and provides a more “normal” texture, and I love them!

These coconut flour chocolate muffins are full of wholesome and simple ingredients. Here are the basic steps to make this muffin recipe. The recipe card further down has the exact measurements. Some coconut flour muffin recipes have you mix the wet ingredients and the dry ingredients separately. These are not those muffins. Yay for fewer steps!

Prepare your muffin tin by filling it with cupcake liners or greasing each hole.
Add the eggs, cocoa powder, coconut flour, coconut oil, baking soda, vanilla extract, sea salt, and honey to a medium bowl (or a large bowl if you are making a double batch). Mix using an immersion blender. You could use a food processor but less mess is always best in my book.
Add the bananas to a small mixing bowl or large measuring cup. Smash until smooth using a potato masher or large fork.
Add chocolate chips and mashed bananas to the batter. Stir gently to combine.
Divide the batter evenly in the prepared muffin tin.
Bake muffins and enjoy!

Chocolate Coconut Flour Muffin Tips & Tricks

Use large eggs that are room temperature. Baked goods have better and more consistent results when you do so. If you have your own chickens you may have to increase the eggs by one or two if your hens lay eggs that are on the smaller side.

Unlike some recipes that use baking soda as the leavening agent, this recipe calls for baking powder. It has a milder taste that can sometimes come through when using baking soda.

You also might be thinking: “you said that coconut flour is “thirsty” why isn’t there much liquid in this recipe?” The great thing is that between the eggs, coconut oil, and bananas it already has all the liquid it needs! Some coconut flour recipes use eggs and liquid, this just isn’t one of them.

Coconut flour is more expensive than regular flour. So if you are new to baking with it there might be a bit of an extra cost upfront to buy your first bag. You can buy it in bulk and save a lot of money! Plus a little coconut flour goes a long way since you are using about 1/4 of what you would use in a standard recipe.

How do I store coconut flour muffins?

You can store these double chocolate muffins in an airtight container for three days. After that, you will want to transfer them to the refrigerator. Good luck having them last that long though, in my house they get gobbled up!

To freeze these muffins, place them on a cookie sheet and freeze until they are solid. Then transfer them to a freezer-proof container or resealable freezer bag. They will remain fresh for 3-5 months.

For trips I like to pack individual lunch bags with reusable containers of snacks, and the minimal mess is contained.

45 degree shot of some coconut flour chocolate muffins on a piece of parchment paper with a cup of tea and muffins on a cooling rack in the background

Can I substitute the coconut flour for another flour?

There are a lot of great flours out there, I even have recipes that use some of them but these are coconut flour muffins. Coconut flour is unique in the world of healthy flours, so there is not a one-to-one substitution that works well.

That’s why you won’t find whole wheat flour, all purpose flour, almond flour, or tapioca flour in these chocolate coconut flour muffins.

Can these be made with an egg replacer?

Eggs are such an important part of this recipe that I don’t use an egg replacer. I’ve never tested this recipe with any of them. For best results, use eggs.

If you do try a swap like flax egg or something else please let me know in the comments! It’s awesome when we can learn from each other.

What can I use instead of honey?

Maple syrup is a great one-to-one ratio for honey. They are both liquids and full of amazing nutrients. It would be a more equal substitution than using a granulated sweetener like coconut sugar.

a close up shot of a coconut flour chocolate muffin being held up to the camera

What can I use instead of coconut oil?

Melted coconut oil works well in this recipe since coconut since the recipe already calls for coconut flour. If you’re concerned about a coconut flavor, you can use refined coconut oil, which works great.

Possible subsitutions would be:

Melted butter. Butter is always delicious, right?
Olive oil. Look for lighter flavored olive oil. The flavor of the chocolate and banana will mask any flavor that might come through from the olive oil.

Fun twists on these coconut flour muffins

The first time you make this recipe try making it the way it is written. That way you will know how it is supposed to turn out before you start making variations, then the next time you can play around with it a bit.

Here are a few simple and fun twists that you could try. Just remember that they are untested:

Mini muffins. Bite-sized muffins would be fun to try. Perfect for the little people in your life. This recipe would yield about 30 miniature muffins. Start checking on them after 10 minutes since the smaller size will make them bake more quickly.
Coconut flour banana bread. If you want to have a few minutes of prep time you could pour the batter into a small greased bread pan. The trade-off will be a longer cooking time. You would want to start checking for doneness after 30 minutes.
Try stirring in a spoonful or two of almond butter, peanut butter, or nut butter of your choice.

a close up shot of coconut flour chocolate banana muffins on a cooling rack, shot on an angle

What is the best way to enjoy these chocolatey muffins?

Really, these coconut flour chocolate chip muffins are the perfect grab-and-go snack or meal. That’s how we enjoy them most of the time but here are some ways to serve them.

Pair with Greek yogurt for a wonderful healthy breakfast.
Serve with a cold glass of milk or a substitute like almond milk.
Use heavy cream to make homemade whipped cream and serve each “cupcake” with a large dollop of whipped cream.

They’re the perfect snack to go alongside some fruits and veggies, and maybe some crackers and hummus. Since they’re grain-free, you can include another convenient grain-based snack without worrying about overdoing it on the heavy carbs.This isn’t a true low carb chocolate muffin recipe but there are significantly less than a traditional recipe.

Looking for more healthy snack ideas?

Pumpkin Spice Coconut Flour Muffins
15 Clean-Eating Snacks
Feeling adventurous? Try these bright green muffins that will sure to delight the kids. (Can be adapted to gluten-free with gluten-free flour instead of wheat.)
Homemade Kettle Corn
Instant Pot Hummus
And check out this huge list of healthy snack ideas inspiration with this post: 100 Healthy Snack Ideas.