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chocolate chip muffins on a cooling rack

Gluten Free Chocolate Chip Muffins

Gluten free chocolate chip muffins that are healthy! Soft and fluffy gluten free muffins that can be made dairy free.
Course Breakfast
Cuisine American
Prep Time 15 minutes
Cook Time 25 minutes
Servings 12 muffins
Author Lyndsey


  • 2 cups gluten free flour
  • 3/4 tsp baking soda
  • 1/2 tsp salt
  • 1 cup coconut sugar
  • 1/2 cup coconut oil softened
  • 2/3 cup unsweetened applesauce or almond milk divided
  • 3/4 cup dairy free or vanilla greek yogurt
  • 2 eggs
  • 3/4 cup chocolate chips


  • Preheat oven to 425F. Add coconut sugar and coconut oil to a stand mixer bowl or large bowl.  Mix until well incorporated.
  • Add in the eggs, one at a time until fully incorporated. Add in yogurt and vanilla extract to wet ingredients and mix well.
  • Add in 1/3 cup of applesauce or milk.  You will add in the other 1/3 later if batter is too dry.
  • In a separate bowl, mix or sift together the gluten free flour, baking soda and salt. Add the dry ingredients to the bowl of wet ingredients in three parts, mixing slowly each time.
  • If the batter seems to dry, add in either more applesauce or almond milk, starting with a bit and adding until you get a nice moist (but not wet) dough consistency.  Fold in chocolate chips.
  • Line a muffin tin with silicone muffin liners and spray them with coconut oil spray.  Scoop the batter into the liners with a cookie scoop and place in the oven.
  • Bake muffins at 425F for 5 minutes.  Reduce heat to 350F and bake for an additional 20-25 minutes or until a toothpick comes out clean.


Customization Tips:
  • Add 1-2 tbsp cacao powder for chocolate muffins with chocolate chips.
  • Sneak in some extra veggies by adding in grated zucchini.  You may need to reduce the amount of liquid (applesauce or milk) if you add in zucchini.
  • Swap out applesauce for mashed banana to make a gluten free banana chocolate muffin.
  • Bake in a bread pan for 50-60 minutes at 350F to make gluten free chocolate chip bread.
Tools to Make Muffins Easier
  • large ice cream scoop - this helps to make sure all of your muffins are standard in size
  • silicone muffin liners - much easier to use and less wasteful than traditional muffin liners
What temperature should I bake muffins at?  I like to start my muffins at 425F for 5 minutes and then finish them for 20 or so minutes at 350F.  I've found this helps them to be fluffier!
What is the secret to making moist muffins? My secret for moist muffins is yogurt!  I add either Greek yogurt or dairy free yogurt to all of my muffins and breads and it always yields delicious moist muffins.
Do I need baking powder for muffins?  I use baking soda in all of my muffin recipes and it works well!  Baking soda has quadruple the power of baking powder so be sure to convert measurements appropriately before swapping.