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5 from 1 review

Gluten Free Chocolate Chip Muffins

These Gluten Free Chocolate Chip Muffins are your answer to a small batch, gluten free, and naturally sweetened bakery style muffin!  This is an easy small batch recipe for 4 tender muffins made with an almond flour blend, perfectly sweetened with coconut sugar, and studded with plenty of chocolate chips.
Prep Time10 mins
Cook Time13 mins
Total Time23 mins
Course: Breakfast
Cuisine: American
Keyword: Breakfast, Chocolate Chip, Coconut Sugar, Gluten Free, Muffins, Natural Sweetener
High Altitude Adjustment: May not require full bake time. Start checking for doneness at minimum bake time if noted.
Servings: 4 Muffins
Author: Erin Cernich



  • Preheat oven to 425F degrees and adjust the oven rack to the middle position. Line a muffin/cupcake pan with 4 cupcake liners.
  • In a small mixing bowl, sift together the almond flour, arrowroot flour, coconut flour, tapioca flour, coconut sugar, baking powder and soda, and salt.
  • To keep the chocolate chips from sinking - In a small bowl, add the chocolate chips and a couple sprinkles of arrowroot flour to coat the chocolate chips.
  • In a medium mixing bowl, add the egg, yogurt, oil, and vinegar. Stir until well combined and creamy. Sprinkle the dry ingredients over the wet ingredients and stir the batter until no dry streaks remain. It is ok if there are a few lumps. Add the chocolate chips and stir just until mixed. Scoop the batter equally into the prepared muffin liners. Sprinkle the tops of the muffins with Turbinado sugar (if using). You can also add a few extra chocolate chips to the tops of the muffins.
  • 425F degrees for 5 minutesThen reduce the heat to 350F degrees and continue to bake for another 7 to 8 minutes, or until the tops of the cupcakes are golden brown and a toothpick inserted in the middle comes out mostly clean. Cool in the pan set on a wire rack for 10 minutes, then transfer the muffins to the wire rack to cool completely. Enjoy!


  • Bake Temperature – Baking at a high temperature (425F degrees) for the first 5 minutes, then lowering the temperature will make the muffin tops puff up. 
  • 1:1 Gluten Free Flour – I have not tested this recipe with a 1:1 Gluten Free Flour blend.  I would recommend following the recipe for Chocolate Chip Muffins.  Swap the flour 1:1 and the chocolate chips for 1/4 cup of chocolate chips.
  • Non-Gluten Free Alternative – I would recommend following the recipe for Chocolate Chip Muffins.