Dr. Rachel’s Favorite Low-FODMAP Chocolate Chunk or Chocolate Chip Cookies recipe; Gluten-free, Dairy-free

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Who said that gluten-free, low-FODMAP cookies weren’t crisp on the outside and soft and chewy on the inside? They obviously have never tried the recipe for these low-FODMAP Chocolate Chunk/ Chocolate Chip Cookies.

These rich and delicious low-FODMAP Chocolate Chunk/Chocolate Chip Cookies don’t contain gluten or dairy, so this low-FODMAP recipe is sure to please any crowd.

I dare to declare this is the best low-FODMAP chocolate chunk or chocolate chip cookie recipe ever.  These are the CLASSIC Chocolate Chip Cookies you grew up eating, just gluten-free and low-FODMAP to boot!

Stick with traditional round shapes, or try a low-FODMAP chocolate chip cookie-cake for your next big occasion (my kids love these).

Another alternative to beat the summer heat…create your own ‘low-FODMAP chocolate chunk cookie ice cream sandwich’ using your favorite low-FODMAP ice cream or one of my delicious low-FODMAP ice cream recipes (low-FODMAP dark chocolate ice cream and low-FODMAP vanilla ice cream).

You may also love my low-FODMAP Chewy Oatmeal Cookies or low-FODMAP Edible Cookie Dough recipes.  Or check out over 300 more low-FODMAP recipes on the blog.

Be healthy and happy,

Rachel Pauls, M.D.

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

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

Modified from “Gluten-free Baking Classics; Second edition”, Annalise G. Roberts, 2008.

Serves 12 or more; recipe can yield between 24 and 70 cookies depending on size

Bake: 375 degrees F

Prep time: 15 minutes
Bake time: 15 minutes (for 12 cookies per sheet- adjust bake time for smaller cookies)


  • 1 cup vegetable shortening (this low-FODMAP chocolate chunk cookie recipe works best with shortening, using butter will cause the cookies to get too spread out)
  • 1 cup sugar
  • ½ cup dark brown sugar
  • 2 large eggs
  • 1 tablespoon vanilla extract
  • 2 cups & 2 tablespoons Authentic Foods GF Classical Blend flour (check out my low-FODMAP flour bake off blog to see why this is my favorite low-FODMAP flour)
  • 1& ½ tsps baking soda
  • 1 tsp xanthan gum (if not included in your low-FODMAP flour choice)
  • ½ tsp salt
  • 12 ounces chunked semi-sweet chocolate (can substitute chocolate chips if desired)
    • for this recipe I chunked low-FODMAP semisweet chocolate and low-FODMAP 80% dark chocolate for a bit of a variation
  • Cooking spray or silicone baking sheets/parchment for lining baking sheets


  • Preheat oven to 375 F
  • Grease cookie sheet with spray, or if making cookie-cake, grease 9 inch round cake pan and cover with parchment round
    • can also use parchment paper or silicone baking mats
  • Place vegetable shortening and 2 types sugar in bowl of mixer and beat well
  • Add eggs and vanilla, beat at medium until fluffy (about 5 minutes)
  • Add flour, baking soda, xanthan gum and salt
  • Mix at medium speed until well combined, scraping down sides of bowl as needed
  • Add chocolate chunks and mix together by hand
  • Scoop onto prepared cookie sheet, or press into cake pan
  • Can make up to 70 cookies depending on size (I prefer large and made 24 big ones)
  • Place in preheated oven to 375F for about 15 minutes; shorter for smaller cookies
    • About 25 minutes for low-FODMAP chocolate chip cookie-cake (placed in 9 inch cake pan)
    • Watch closely- cookies are done when light golden brown
    • Edges will be crispy when cooled with soft centers
  • Store in airtight container if they last
  • Hint: Dough may also be pre-made, rolled into tube and frozen for 3 months. When ready to bake, cut out low-FODMAP cookies
  • Enjoy as a low-FODMAP chocolate chip cookie cake or low-FODMAP chocolate chunk cookie ice cream sandwiches (for sharing)!

  • Dig in!

Comments Rating 5 (1 review)

6 Responses

    1. Kendra,
      This is fantastic!
      We are so happy to hear from you. It made our day!!
      Can we suggest taking a look at our COOKBOOK available in the US, Canada, UK and Australia?
      THE LOW-FODMAP IBS SOLUTION PLAN & COOKBOOK 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.
      Stay in touch please!

    1. Hi Terry,
      Thanks for the question. We do love using shortening in some of our recipes, it can provide a better result than using butter or other substances in a gluten free version. As mentioned in the recipe, butter may create a more spread out cookie, but chilling these before baking for about an hour will likely help. We buy organic vegetable shortening for our baking needs. Good luck!

  1. This looks incredible!! Is there any chance I can replace the white and brown sugar with palm sugar or maple syrup without ruining the consistency? Sugar tends to really mess up my gut and that causes bad skin reactions. Thank you!

    1. Hi Kris,
      We have only tried the recipe as it is written. Usually changing the sugar would result in an issue with the texture and baking outcome. With gluten-free flours it can be even more challenging. Sorry we can’t help more!

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