Take your breakfast to another scrumptious level with these decadent gluten-free muffins loaded with bold chocolate and coffee flavors. They’re made with simple ingredients that, when combined, create delicious dark chocolate coffee muffins that are free of refined sugars, refined oils, and gluten – with additional tips to make these dairy-free as well.

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Instead of adding oil to this recipe, cooked butternut squash is used in its place to add not only moisture but also vitamins and minerals like vitamin C, magnesium, and potassium. What’s even better – you’d never know the difference! I mean I semi-feel a mommy win here since my kids won’t touch squash of any kind. What they will touch, and devour I might add, are these. I win.


Gluten-Free Dark Chocolate Coffee Muffins


Makes 14 muffins



  • 2 eggs
  • ½ cup whole milk of choice (see note)
  • ½ cup cooked butternut squash (see note)
  • 2 cups almond flour
  • ¾ cup coconut sugar
  • ½ cup cacao powder
  • ¼ cup tapioca flour (see note)
  • ¼ cup instant coffee (see note)
  • ¾ teaspoon baking soda
  • ¼ teaspoon salt
  • ½ cup chocolate chips, optional (see note)



  1. Preheat oven to 350F. Place 14 silicone cupcake liners in cupcake pans and set aside (or use regular cupcake liners or a cupcake pan coated with non-stick spray).
  2. In a mixing bowl, whisk together eggs, milk, and butternut squash until smooth.
  3. In a separate large mixing bowl, combine flours, cacao powder, coconut sugar, instant coffee, baking soda, and salt.
  4. Pour wet ingredients into the bowl of dry ingredients, Mix until well-combined. Stir in chocolate chips, if desired.
  5. Evenly distribute muffin batter into each muffin liner, filling about 2/3 full. Top with chocolate chips for an added chocolate bonus (just do it)!
  6. Bake in the oven for 15-18 minutes, or until toothpick comes out clean when inserted into center of muffins.
  7. Remove muffins from oven and let cool about 10 minutes. Remove from liners and enjoy!



  • I used regular whole cow’s milk. Full-fat milk alternatives, like almond, cashew, coconut, and oat milks, would also work to create muffins free of dairy.
  • You can substitute cooked butternut squash with cooked sweet potatoes, ½ cup melted grassfed butter, or ½ cup melted coconut oil.
  • Use canned butternut squash for quicker muffin prep.
  • You can substitute tapioca flour with coconut flour or oat flour. You can also use 1/3 cup whole-wheat flour but this adds gluten to the recipe.
  • I used this organic instant coffee.
  • I used these chocolate chips – they are free of refined oils, refined sugars, and crap ingredients. They are not sweetened at all, in fact, creating a less sweet chocolate flavor. I recommend using this chocolate if your kids (or yourself) are picky with unsweetened chocolate. Just chop it into small pieces before mixing it into the muffin batter.
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Showing 4 comments
  • Amanda Pont

    I’m interested to try this. I’ll let you know how I go 🙂

    • Nicolette

      I would love to hear how you like them if you end up trying it!

  • Anonymous

    This is the best GF muffin recipe I ever had. I used sweet potato instead of squash . It was soft and moist for days. My friends and family are crazy about it.

    • Nicolette

      Thank you 🙂 I’m so happy everyone likes it!

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