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The Best Gluten Free Chocolate Muffins

The most perfect Gluten Free Chocolate Muffins to ever exist! Dense, rich, chocolate filled muffins are made gluten free with oat flour and coconut flour.

gluten free chocolate muffins with a bite taken out

Let me introduce to you the best gluten free chocolate muffins.

I don’t use those words lightly, and one bite of a muffin and you will understand why!

These muffins are insanely chocolatey, soft and light (not dense or dry), and so satisfying thanks to greek yogurt!

Each rich, chocolatey muffin contains 5g of protein.

two gluten free chocolate muffins stacked

How to make gluten free chocolate muffins

Step 1: Mix together the wet ingredients first: yogurt, maple syrup, eggs, vanilla extract, and melted coconut oil.

Tip: allow the coconut oil to cool slightly before adding to the other ingredients. If the air is too cold and you add the oil in hot, it may turn back to solid form.

What Can I use Instead of Maple Syrup?

You can substitute another liquid sweetener, such as honey or agave.

Step 2: Whisk together dry ingredients: oat flour, coconut flour, cocoa powder, salt, baking soda, and baking powder in a separate bowl.

Gluten-Free Flour

Many gluten free flour blends can have varying results.

I have come up with a fool proof gluten free flour combination that I have used in many recipes like these gluten free chocolate chip muffins, and gluten free chocolate mug cake.

Oat flour and coconut flour are both easy to find, and affordable.

How to make your own oat flour

Can’t find oat flour? No problem!

Simply buy gluten free rolled oats, pop them in the blender, and blend until they turn into flour.

gluten free chocolate muffins from an overhead view topped with melted mini chocolate chips

Step 3: Add the dry ingredients to the wet, and use a rubber spatula to stir until just combined.

Step 4: Fold in the chocolate chips, then fill the muffin liners with the batter

Step 5: bake your gluten free chocolate muffins for 15-18 minutes, until a toothpick inserted comes out clean.

Why we love these gluten free chocolate muffins

Texture is everything with gluten free recipes, and this is the best texture I have ever been able to create!

These taste like a cross between the most moist and flavorful chocolate cake and your favorite brownie. 

They don’t fall apart, and aren’t too sweet (I love using Enjoy Life chocolate chips for this recipe).

I used mini chocolate chips for a better distribution of melted chocolate on the inside, ensuring that every delicious bite is chocolate packed!

I love grabbing one of these for a healthier dessert or mid day snack!

two stacked chocolate muffins

Tips for muffins that do not stick

I recommend using parchment paper muffin liners anytime you make muffins.

Absolutely nothing will stick to parchment paper, so the muffins just come right off!

If you do not have these, spray your regular muffin liners with cooking spray before adding the batter.

three gluten free chocolate muffins

If you are prone to reaching for sugary cereal to curb a morning sweet tooth, these would be the perfect breakfast for you! 

Each muffin is less than 200 calories and has a whopping 5 grams of protein in it. 

Two chocolate muffins for breakfast? Yes,please!

one chocolate muffin stacked on two other muffins

More gluten free muffin recipes

single gluten free chocolate muffin in a parchment paper muffin liner
image with text "fudgy chocolate gluten free muffins"

Gluten free chocolate muffins recipe

The BEST gluten free chocolate muffins - perfectly soft, light, not dense, not dry, and not too sweet. They are literally the perfect chocolate muffin!

Gluten Free Chocolate Muffins

Joy Shull
The best gluten free chocolate muffins recipe with yogurt. Dense, rich, extra chocolate filled muffins made gluten free with oat flour and coconut flour.
4.47 from 39 votes
Prep Time 10 minutes
Cook Time 15 minutes
Total Time 25 minutes
Course Gluten Free
Cuisine American
Servings 12 muffins
Calories 193 kcal


  • 1 cup plain 0% greek yogurt
  • ¼ cup coconut oil melted
  • 2 eggs
  • 1 tablespoon vanilla extract
  • ¼ teaspoon salt
  • 1 teaspoon baking powder
  • ¼ teaspoon baking soda
  • ½ cup semi sweet mini chocolate chips
  • ½ cup pure maple syrup
  • ¾ cup gluten free oat flour
  • cup coconut flour
  • cup cocoa powder


  • Measure ¼ cup of coconut oil then melt in a microwave safe bowl until liquid (around 20 – 30 seconds). Allow to cool slightly before mixing with the other ingredients.
  • In a large bowl, whisk together yogurt, maple syrup, eggs, vanilla extract, and melted coconut oil until well combined
  • In a separate bowl, whisk together oat flour, coconut flour, cocoa powder, salt, baking soda, and baking powder
  • Add the dry ingredients to the wet, and use a rubber spatula to stir until just combined
  • Fold in the chocolate chips
  • Line a muffin tin with parchment paper muffin liners (these will ensure the muffins do not stick) or spray regular muffin liners with cooking spray
  • Distribute batter evenly into the 12 cups
  • Top each muffin with additional mini chocolate chips, if desired
  • Bake the gluten free chocolate muffins at 400 degrees for 15 – 18 minutes, until a toothpick inserted comes out clean


Serving: 1gCalories: 193kcalCarbohydrates: 24gProtein: 5gFat: 9gSaturated Fat: 6gPolyunsaturated Fat: 2gCholesterol: 32mgSodium: 135mgFiber: 2gSugar: 15g
Tried this recipe? Tag me on instagram @buildyourbite and hashtag #buildyourbite!Let us know how it was!

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Recipe Rating


Tuesday 8th of February 2022

Can this be made without eggs? We have an allergy to eggs.


Saturday 13th of March 2021

Absolutely love these. They taste like brownies. I substituted plain unsweetened coconut yogurt and they turned out great. Also, added additional baking time due to living at altitude (Denver).

Joy Shull

Tuesday 16th of March 2021

I'm so glad you enjoyed the recipe!


Tuesday 28th of July 2020

Made these but didn't have yogurt so subsituted half of the greek yogurt for sourcream and half for beet puree. No one knew that it had beets in it and they loved it! Thanks so much for these delicious gluten free recipes with simple gluten free flours!

Joy Shull

Thursday 30th of July 2020

So glad you enjoyed the recipe Gabriella!


Sunday 26th of April 2020

I substituted vanilla greek yogurt for plain because it was all I had and it was DELICIOUS!!!!

Amy jo Johnson RN

Wednesday 22nd of January 2020

Can I use almond yougert? I can’t have milk!