The Best Gluten-Free Chocolate Muffins
Chocolate,  Breakfast,  Desserts,  Snacks

The Best Gluten-Free Chocolate Muffins (Easy + Vegan option!)

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These Gluten-Free Chocolate Muffins are delicious! They’re easy to make and extremely fluffy and moist. All you need is one bowl and some simple ingredients. You can make them mini muffins to serve at social gatherings or for kids too. Dairy-free with a vegan option!

Yield: 9

The Best Gluten-Free Chocolate Muffins (Easy + Vegan Option!)

The Best Gluten-Free Chocolate Muffins

These Gluten-Free Chocolate Muffins are so delicious! They’re easy to make and extremely fluffy and moist. All you need is one bowl and some very simple ingredients. You can make them mini muffins to serve at social gatherings or for your kids too. Dairy-free with a vegan option!

Prep Time 10 minutes
Cook Time 20 minutes
Total Time 30 minutes



  • 1 egg or 1 flax egg (1 Tbs. ground flax + 2 Tbs. water. Let thicken for 5 minutes.)
  • ½ cup coconut sugar
  • ¼ cup refined coconut oil *melted
  • ¼ cup plain non-fat Greek yogurt or non-dairy yogurt of choice
  • ¾ cup plant-based milk
  • 1½ tsp. vanilla extract



1. Preheat oven to 350 F. and grease 9 muffin tins (or 26 mini muffin tins) with coconut oil. You may also use paper muffin liners or silicone muffin liners.

2. In a medium bowl add the egg, coconut sugar, and coconut oil. Mix until smooth, then add in yogurt, plant-based milk, and vanilla extract. Mix until smooth.

3. Add in almond flour, gluten-free flour, cacao powder, pink salt, and baking powder. Mix until combined, then fold in ⅓ cup chocolate chips.

4. Fill 9 muffin tins (or 26 mini muffin tins) ¾ full with batter. Top with remaining chocolate chips. Bake at 350 F. for 17-20 minutes (10-12 minutes for mini muffins) or until a toothpick comes out clean. Allow to cool at least 20 minutes in muffin tins. Then carefully twist muffins to loosen them and remove from muffin tins. Enjoy! Store in an airtight container on the counter for up to 5 days, in the refrigerator for up to 8 days, or freeze for up to 3 months.

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Nutrition Information:


9 muffins

Amount Per Serving: Calories: 253Total Fat: 14.1gCarbohydrates: 27.8gNet Carbohydrates: 23.9gFiber: 3.9gSugar: 17.3gSugar Alcohols: 0gProtein: 4.2g

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More Healthy Chocolate Recipes

Healthy Vegan Chocolate Sauce

Dairy-Free Chocolate Pudding

Chocolate Crinkle Cookies (gluten-free!)

Vegan Hot Chocolate

Fudgy Zucchini Brownies

best gluten-free chocolate muffins recipe

The Best Healthy Chocolate Muffins

If you love a nice moist, fluffy chocolate muffin, this is the recipe for you. Just like my Healthy Lemon Poppyseed Muffins recipe, or my Healthy Chocolate Chip Pumpkin Muffins, these muffins are secretly healthy, but you would never know. They are perfectly sweetened and absolutely delicious and you can make them mini size!

Gluten-Free Chocolate Chocolate Chip Muffins

I love creating gluten-free secretly healthy recipes here at the Secretly Healthy Home. You know it’s my jam. And if you know me, you know that I LOVE chocolate everything. So you’re in the right place for gluten-free and chocolate. If you’ve tried my healthy chocolate sauce, dairy-free chocolate pudding, zucchini brownies, or gluten-free chocolate lava cakes, you know what I’m talking about. This gluten-free double chocolate muffin recipe is no different, my friends!

moist chocolate muffins gluten-free

How To Make Gluten-Free Chocolate Muffins

Like I said before, you only need one bowl for this healthy muffin recipe. I hate using multiple bowls for baking. If you feel the same way, then you definitely need to check out my Healthy Baking Course. I teach you all the simple tips and tricks to make healthy baking easy! To make these chocolate muffins you simply mix all the wet ingredients and then all the dry. Fill up your muffin tins and bake! Full instructions are in the recipe above 🙂

Can I Make These Chocolate Muffins Mini Size?

Absolutely you can make these chocolate muffins mini size! Just use a mini muffin pan. This is my favorite one from amazon! I’m obsessed with it and I didn’t think I would use it as much as I do. Honestly, I like making these muffins mini more than regular. They’re the perfect kid snack, treat when friends come over, or dessert! The baking time will vary on the smaller muffins. Bake them for 10-14 minutes until a toothpick comes out clean.

vegan chocolate muffins

Gluten-Free Chocolate Muffins Recipe

I love making gluten-free recipes for all my gluten-intolerant friends. I am not gluten-free personally, but creating secretly healthy recipes usually ends in a gluten-free recipe, and I’m not mad about that. This recipe uses a combination of gluten-free flour and almond flour to make the perfect chocolate muffin. This “flour” combination gives the muffins fluff and also gives them moisture and a very tender texture. I’m sure you’re going to love them!

Can I Make These Healthy Chocolate Muffins Vegan? I haven’t tested making these muffins with a flax egg, but I’m sure it will work. Just replace the 2 eggs with 1 flax egg (1 Tbs. ground flax + 2 Tbs. water. Let thicken for 5 minutes). Let me know if you try this! I’d love to know how they turn out. And if you’re looking for more healthy vegan recipes, definitely check out my Homemade Chocolate Sauce, Chocolate Crinkle Cookies, Fudgy Zucchini Brownies, and so many more!

healthy chocolate muffins

Reasons To Love These Gluten-Free Chocolate Muffins?

  1. Ridiculously easy to make! Just pop everything into a mixing bowl, mix it up, then bake and enjoy!
  2. Perfect amount of fluff and moisture. These gluten-free muffins are fluffy without being too dry or dense. They are perfectly moist!
  3. Flavor explosion. The chocolate flavor and chocolate chips in these muffins really take them to a whole new level.
  4. Super healthy and filling. Since these muffins have healthy ingredients in them, they will keep you fuller longer and won’t spike your blood sugar as badly!
  5. High in fiber. Ya gotta love oats for being such an amazing source of complex carbs and fiber. The perfect way to kick start any day!
  6. There are limitless add-ins for these chocolate muffins! Before baking these healthy chocolate muffins, you can add in shredded coconut, blueberries, strawberries, chocolate chips, or whatever your heart desires!
  7. Toddler and kid-friendly! Kids absolutely love these muffins, especially if you make them mini. They are the perfect size for kids and adults alike!

Happy Gluten-Free Chocolate Muffin Bakin’!

best healthy chocolate muffins

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