Delicious Low-FODMAP Chocolate Chip / Chunk Muffins; Gluten-free, Dairy-free

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This recipe is the best I’ve found for low-FODMAP Chocolate Chunk (or chip) muffins.  Light and moist with the melted chocolate in every bite.  You cannot tell this is gluten-free or low-FODMAP.

This recipe yields low-FODMAP Chocolate Chunk muffins that rival my favorite cafe for breakfast treats (Starbucks).  My sons are the toughest judges and they agree!  They remind me so much of a low-FODMAP Chocolate Chunk Cookie (see my recipe) .

For over 300 more low-FODMAP recipes, check out the blog.  You may also love my low-FODMAP Blueberry Muffins and my low-FODMAP Pecan Cinnamon Crumb Muffins.

Be healthy and happy,

Rachel Pauls, MD

Low-FODMAP Chocolate Chunk Muffins; Gluten-free, Dairy-free

Although this recipe has not been tested, a single serving should be low-FODMAP based on the ingredients.

Serves 12 muffins

Prep time: 20 minutes

Bake time 18-22 min (*as ovens vary, begin checking about 3-5 minutes prior to end time.  You want the muffins to be somewhat moist in the middle as they will continue baking)

Total time: 45 minutes

Bake 350 F


  • 2 cups low-FODMAP, gluten-free flour (I use Authentic Foods GF Classical Blend- the results are so consistent!  Check out my low-FODMAP bake off blog to see why)
  • 2/3 cup sugar
  • 1 tablespoon baking powder
  • 1 teaspoon baking soda
  • 3/4 teaspoon xanthan gum if not added to your flour choice
  • 1/4 teaspoon salt
  • 7 tablespoons low-FODMAP milk (almond milk or lactose-free)
    • this is 1/2 cup minus 1 tablespoon
  • 1/2 cup canola oil
  • 2 large eggs
  • 1 teaspoon vanilla extract
  • 1 cup semi-sweet chocolate chunks plus extra for topping
    • Enjoy Life brand makes dairy-free chocolate chunks in a ready-made bag!  Easier than chopping


  • Preheat oven to 350 F
  • Grease muffin tin with vegetable shortening or use muffin cups
  • Mix low-FODMAP flour, sugar, baking powder, baking soda, xanthan gum in large bowl
  • In another medium bowl or large measuring cup, mix 7 tablespoons low-FODMAP milk and 1/2 cup oil
  • Add eggs and vanilla to milk/oil mixture and beat together
  • Place the liquids into the flour mixture and stir until just combined
  • Fold in chocolate chunks
  • Scoop muffin batter into cups/tin to 2/3 full
  • Sprinkle more chocolate chunks on the tops
  • Bake about 18-22 minutes, will be light golden
    • my oven took exactly 18 minutes
  • Allow to sit about 5 minutes then transfer to a rack to cool
  • Super fun to eat…

  • These are so soft and moist inside…

  • My 10 year old gobbled these low-FODMAP Chocolate Chunk muffins!  He said “Mommy, you outdid yourself!”

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