Low-FODMAP Five Minute Chocolate Chip Microwave Cookie; Gluten-free

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Sometimes I find myself searching in the pantry for a low-FODMAP sweet treat and feel frustrated that I have nothing easy to grab. My low-FODMAP Mug Cakes (like my low-FODMAP Pumpkin Mug Cake, low-FODMAP Chocolate Mug Cake and low-FODMAP PB & J Mug Cake) usually fill that void.  But sometimes I crave a low-FODMAP Chocolate Chip Cookie.

So I created a low-FODMAP 5 Minute microwave chocolate chip cookie recipe.  For those times when you just want to have one.  How can you say no to a warm, melty, rich and delicious low-FODMAP Chocolate Chip Cookie?

Now you can enjoy this low-FODMAP Chocolate Chip Microwave Cookie too. This low-FODMAP recipe results in an ooey, gooey sweet and moist low-FODMAP Chocolate Chip Cookie in under 5 minutes!  So easy. Make it in a mug or a ramekin- it works either way.

You may also love my low-FODMAP Chocolate Chip Cookies and low-FODMAP No-Bake Energy Bites.  Or check out over 300 more low-FODMAP recipes on the blog, IBS-friendly!

Be healthy and happy,

Rachel Pauls, MD

Five Minute Low-FODMAP Chocolate Chip Microwave Cookie; Gluten-free

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

Serves: 1-2

Prep time: 2 minutes

Cook time: About 1 minute

Equipment: Microwave, mug or ramekin


  • 2 tbsp butter
  • 1 large egg yolk
  • 1 tbsp white sugar
  • 1 tbsp dark brown sugar
  • ¼ tsp vanilla extract
  • Pinch of kosher salt
  • 4 tbsp low-FODMAP, gluten-free flour (I use Authentic Foods GF Classical Blend for best results- see my low-FODMAP bake off blog for my reasons!)
  • ¼ tsp xanthan gum
  • ½ tsp baking powder
  • 2 tablespoons (about 30 g) semisweet chocolate chips


  • Melt butter in the microwave for about 20 seconds, then set aside
  • In a bowl or mug, place egg yolk and 2 sugars and mix well to combine
  • Add butter and all remaining ingredients except chocolate chips and combine well.
  • Stir in chocolate chips (reserving a few for sprinkling if desired), and give a final stir
    • Mixture should look like cookie dough
    • Add a few chocolate chips to the top of the low-FODMAP cookie dough if you like
  • Cook in microwave 40-60 seconds
    • Mine took the full minute
    • If you like your low-FODMAP cookies a little undercooked, then adjust as necessary
  • Serve immediately, top with low-FODMAP Ice Cream or low-FODMAP Whipped Cream

  • Do you want the next bite? 😉

Comments Rating 5 (8 reviews)

24 Responses

  1. This was honestly awesome & so quick!! I didn’t have chocolate chips so I subbed in 1/2 tablespoon of peanut butter & it was great!

  2. Ingredients

    I haven’t made them yet but I’m sure they are good, hence the 5 stars. But I’m wondering if the xanthan gum is a necessary ingredient?

    1. Hi Jon!
      Thanks for the question, and we appreciate the stars 🙂
      Since there is such a scant amount of flour in the recipe, it is likely the cookie will still turn out great without the xanthan gum. We haven’t tried it that way but please let us know if you do!!
      Have a wonderful day.


    Day two of this elimination diet and this was sent by the goddess herself. I was feeling so down about everything until stumbling upon this. Ate the entire thing and my only complaint was that there wasn’t more!

    Thank you for this recipe and so many more! Im excited to explore more!

    1. WOW Taylor, that’s awesome!
      Not sure what ‘goddess’ you are referring to, but we are more than thrilled to make your journey easier. We have so many delicious meals and treats to choose from! So good to hear from you!!
      You may also be interested to know 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 🙂

  4. This is such a great recipe! It is easy, simple, and delicious! If you all are going for something healthier than this recipe, just substitute some ingredients! For example, real sugar —> coconut sugar. Besides that, this was great! 🙂

      1. I will, especially with recipes like yours! How did you respond so quickly?! You must really care about the feedback you receive! 🙂

        1. You are sweet! Yes, we do care 🙂
          Talking to our readers is one of our most favorite things.
          Thanks again

  5. Rachel Pauls Food

    So easy. Loved it! Will look for more of your recipes. I am just getting started.

  6. Rachel Pauls Food

    Is it possible to get the nutrition facts for this cookie? I would really appreciate that. Thank you.
    Low-FODMAP Chocolate Chip Microwave Cookie; Gluten-free

    1. Hi Sandra!
      We are so happy you enjoyed the recipe!
      Can we suggest taking a look at our COOKBOOK available in the US, Canada, UK and Australia? It may also be a great asset to you!!
      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!!
      Unfortunately, we are not able to provide nutritionals for our recipes.
      Have a wonderful day ?

  7. Love this but kinda crumbly

    I loved this recipe my only issue was that it came out crumbly which I don’t mind but are we suppose to let this set for a few mins?

    1. Hi Annie,
      All gluten-free flours behave differently, so if you did not use the same flour as we did, then it could be crumbly. Also, in general, microwaves will continue cooking your food for a short while after they stop. Its not a bad idea to let your food sit for a minute to continue the cooking process. However, we can’t say if that’s the reason for crumbling, because it may actually be that you slightly overcooked the cookie, rather than undercooked it. Experiment with your microwave oven, as they vary considerably in their power levels. Thanks for your comments!

  8. Awesome!!!

    I am new to the low FodMap diet and miss my chocolate chip cookies!! This was the next best thing!!! Thank you for sharing 🙂

    1. Hi Gina,
      So happy you found us! We hope our recipes and our low-FODMAP food products will also show you how delicious the low-FODMAP lifestyle can be. Stay in touch!!

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As an IBS-sufferer myself, I know how badly you want to feel healthy and happy. I’ve spent over a decade researching IBS and FODMAPs, and my recipes and guidance will help you succeed.

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