Prep: 10 mins

Cook: 6-8 mins

Yields: 12 servings

A SIBO friendly chocolate chip cookie recipe. It's the perfect afternoon treat, plus it makes for a great dessert for bringing along to parties and picnics.

SIBO Chocolate Chip Cookies Recipe 800x800


  • 1 ¼ cups almond flour (you could substitute ¾ cup coconut flour)
  • 4 tbs (2.5 oz) butter, chilled, cubed
  • 2 tsp honey (or a sweetener you can tolerate)
  • 1 tsp vanilla
  • 6 oz 100% cacao chocolate, unsweetened, chopped


  • Pre-heat your oven to 350F.
  • Place the almond flour into a bowl. Add the butter. Mix together with your hands until combined (or you could do this in a food processor). Add the honey and vanilla and mix well. Stir in the chocolate until combined.
  • Line a baking tray with parchment paper. Spoon 1 teaspoon at a time of mixture onto the tray. Leave space between them as they will expand during cooking. Flatten with the back of a spoon.
  • Place in the oven for 6-8 minutes. They will feel very soft to the touch when they come out of the oven, but will firm up as they cool down.
  • Enjoy warm while the chocolate is still melted.
  • These are best enjoyed on the day of baking. Freeze any remaining cookies and re-heat in the oven for a few minutes to refresh them.

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21 thoughts on “Chocolate Chip Cookies”

  1. Hello!
    Thank you for this recipe, I have been baking a lot of yours 🙂
    With this one for one reason didn’t work out and had to through them away, not sure why but the chocolate completely melted over the whole mixture while cooking – how do you keep yours hard?

  2. I made these with a couple of departures from the recipe and loved it! My first SIBO friendly treat. Thank you! I did half butter half coconut oil. I also did 1 cup almond flour and 1/4 cup finely shredded coconut and used 1 tsp of honey and one smashed banana for sweetness. being Iranian, added a couple tsp of cinnamon as well. As author says cookies were soft when then came out and a bit harder when cooled.

  3. Oh my what a disappointment. Do not know what went wrong. There didn’t seem to be enough of the flour mixture for the amount of chocolate. I also used cacao nibs and it didn’t melt – this is what I used for the chocolate granola! Tiny little hard nuggets of nasty.

    Something seriously went wrong.

    1. Rebecca Coomes

      Hi Jill
      Cacao nibs are the problem! They don’t melt and won’t add any extra moisture to the mixture. This recipe calls for 100% chocolate, which also contains fat, which helps make these cookies more moist.

  4. Mine turned out very bad, they crumbled I used coconut flour and found it terrible, very disappointed.
    What could I do to not let this happen again??

    1. Rebecca Coomes

      Coconut flour has a different absorbency rate to almond flour so you might need to play around with the quantity to get it right. You might have also needed a bit more moisture if they didn’t hold their shape. I find it can depend on the brand you use, how finely ground it is, whether it’s cold or hot on the day you bake. Can you tolerate almond flour?

  5. Thank you!! I stumbled on this cookie recipe looking for a SIBO friendly cookie for my husband. I’ve made them twice now and he loves them. Much appreciation for your blog here, I’ll explore some of your other recipes.

    1. I have tried using coconut oil with these but it doesn’t work as well. You could try and see how it goes? It might work better for you than it did for me.

    1. It depends on what diet you’re following and how sensitive you are to sugar. Some people can tolerate a small amount of dark chocolate which contains sugar, but others need to avoid it. If you want to make your own sugar free chocolate, you can always use my sugar free dark chocolate recipe and make your own at home. I make my own chocolate all the time now, because that way I know exactly what’s in it.

    1. Hi Annie
      When I’ve made these I was able to get 12 cookies out of my mixture. Did you follow the quantities exactly?

      1. I have been a baker for a life time . I found the chocolate chip cookie recipe a desaster. They didn’t turn out very well they fell apart whenI tried to transfer to the rack to cool. chocolate was dripping all over the place took much more time than indicated to prepare as well.

        1. Hi Millie
          I’m sorry to hear these didn’t work out for you. They are different to ‘regular’ cookies as they don’t contain all the sugar that makes them gooey and chewy. SIBO baking is definitely a different experience than ‘regular’ baking, and I had to learn to adapt my baking accordingly.
          Without seeing what you did, I’m not sure why these didn’t turn out well for you. Did you use all of the ingredients listed and by the measurements in the recipe?

  6. Hi Rebecca,

    Followed this recipe and the cookies did not come out well at all. Actually had to throw them away. The consistency was not right and the batter was pretty much impossible to stick together. Wondering if something was left out of the instructions or of you had any tips? Also, they were extremely bitter..maybe need to add more honey? Love your recipes and utalize your website all the time.Thank you!

    1. Hi Sophia
      I’m sorry these didn’t work out for you. I’m not sure where it went wrong unfortunately, because I wasn’t in the kitchen with you. These aren’t an overly sweet cookie, but you are welcome to add more honey to them if you like them sweeter.
      SIBO baking is different to regular baking, because we don’t use regular flour and sugar, so you may need to get used to new ‘SIBO’ consistencies. But when I’ve made these cookies, they do hold together and look like a cookie.

  7. Hi Rebecca – thanks so much for sharing this recipe. How would you describe the texture of these cookies? Are they soft and chewy, or more crunchy?

    1. Hi Melissa
      They’re in between soft and chewy and crunchy! When they’re first out of the oven they’re softer, but then do firm up a bit as they cool. However, they’re not a traditional crunchy cookie. Hope that helps?

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