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!”

Comments Rating 4.2 (5 reviews)

13 Responses

  1. Yum!

    Mine were a bit overdone in 18 mins but could be my oven or that I was converting to celsius. Will definitely be making them again!
    Believe it or not 1 cup was actually too much choc (I used chips).
    Thanks for the great, easy, recipe!

    1. Thanks for the comment! As ovens vary, the directions suggest checking 3-5 minutes prior to the end time to ensure you don’t overbake these (at the top under bake time). Sorry you must have missed that. Better luck next time, glad you enjoyed the recipe.

  2. Delicious!

    These muffins are delicious! Disappeared pretty quickly! The mix needed some extra almond milk and they turned out great. Perfect for the whole family.

    1. Awesome to hear Tina!
      It is always good to trust your instincts if it needs a little fine tuning. Some eggs are larger than others, and the flour measurements may vary slightly when using a cup rather than weight system 🙂
      Glad they worked out well and hope to hear from you again!!
      We think you may also want to know that we have a cookbook coming out October 6, 2020!
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  3. So good!

    These seem so decadent! They were absolutely delicious. I couldn’t resist sampling one while still warm. Ooey gooey delight. Thanks for the recipe!

    1. CRS,
      Thanks so much! Love hearing from you 🙂
      You may also be interested to learn that we have a COOKBOOK available in the US, Canada, UK and Australia.
      THE LOW-FODMAP IBS SOLUTION PLAN & COOKBOOK is the ONE thing that will take you through the entire FODMAP journey and share more than 100 recipes that prep in 30 minutes or less! It also has a meal plan, grocery list and many more tips. Click here for details on the BEST low-FODMAP book available 🙂
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  4. Help

    I’m very confused. I followed the recipe exactly and my batter ended up the consistency of cookie dough. I added extra oat milk to try and then it out but ended up giving up and putting them in the oven. They’ve baked for 20 mins so far and haven’t risen or left their doughy form at all.

    1. Andrea,
      Sorry, but we aren’t sure what went wrong…did you use all the ingredients? This recipe is tried and true, it has been baked many times in our household and is very consistent. Hope you have better luck next time.

    2. Check that your baking powder isn’t old or hasn’t expired. That may be why you are not getting the leavening. Maybe add some acid (vinegar or lemon juice) to activate it.
      The humidity level of your environment can impact your ingredients as well.

  5. I’m low fodmap and dairy free so made these without chocolate and they were so good! Next time I’m gonna add cinnamon hehe
    Thanks so much for a simple low fodmap recipe ❤️

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