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Meal Type ยป Desserts ยป Gluten Free Brookies

Gluten Free Brookies

Claire Cary

By

Claire Cary

5 from 1 vote
January 28, 2026
Jump to Recipe

These gluten free brookies combine two of the best desserts- a layer of fudgy gluten free brownies topped with a layer of thick chocolate chip cookies. They’re a rich, indulgent dessert that will impress all of your friends.

three gluten free brookies stacked on each other

I am all for a healthier dessert like my chocolate chip protein cookies when the time is right, but most of the time I want the fully indulgent, sugary, buttery desserts. These gluten free brookies are exactly that. They have a thick layer of gluten free brownie as the base and are topped with a chewy chocolate chip cookie top.

It’s a more involved recipe than some of my other baked goods because we essentially have to make two separate things, but I promise the end result is well worth the time and the dirty dishes! If you love this recipe, try my marble chocolate chip cookies next!

Tips before we get started!

  • I used semi-sweet chocolate chips, which I recommend, but for a richer flavor, you can swap with dark. This works for both the cookie layer and brownie layer.
  • Be sure to let the brookies cool completely before slicing so they slice nice and clean and don’t crumble.
  • When adding the cookie layer on top of the brownie layer, be sure to divide the dough and flatten and then add it on top. Don’t try to spread it all out on top of the brownie batter or it won’t be even!
ingredients in bowls with labels

How to make gluten free brookies

Preheat the oven to 350 degrees Fahrenheit. Line a 9×9 baking pan with parchment paper and set aside.

To make the brownie layer: in a small bowl, add the butter and chocolate chips. Melt in the microwave in 30 second increments, stirring between each until fully melted.

In a second bowl, add the sugar, vanilla and egg. Use an electric mixer to beat for about 30 seconds. Add in the chocolate mixture and beat to combine. Fold in the cocoa, flour and salt. Mix until well combined. I opted against adding extra chocolate chips to this layer, but you can add about 1/2 cup to the batter if you like! Transfer to the prepared baking pan and spread smoothly.

two images showing how to make the brownie layer

To make the cookie layer: Add the softened/room temperature butter, white sugar and brown sugar to a mixing bowl and beat with an electric mixer for about 30 seconds. Add in the egg yolk and vanilla and beat to combine.

Add in the flour (spoon and level to measure), baking powder, baking soda and salt. Mix to combine. Fold in the chocolate chips.

Divide the dough into about 4 large balls. Flatten each ball in your hand and place on top of the brownie layer, pressing into the corners of the pan. Take any leftover dough and press to fill in any gaps. Top with extra chocolate chips if desired. Bake for 25-30 minutes or until the edges are just golden brown and the center looks set. Let cool fully in the pan, then slice and enjoy! Try my gluten free brownie cookies next!

two images showing how to make the cookie layer

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Make it a slutty brownie!

A slutty brownie is essentially a brookie but with the addition of oreos. Since Oreo makes a gluten free version, you can add 16 oreos to the top of the brownie layer before adding on the cookie layer. No other changes are needed! So it’ll be a cross between my gluten free oreo brownies but now with a layer of cookie on top!

dough in a pan before baking

Ingredient swaps

Flour. I opted to use the Bob’s Red Mill gluten free 1:1 baking flour, but King Arthur also works well. Just make sure you are using a blend with xanthan gum for both the cookie and brownie layers.

Butter. You can swap for a dairy free butter, but for the best flavor, I don’t recommend coconut oil or another type of oil here.

Sugar. For the cookie layer, you need a mix of white sugar and brown sugar, which add moisture but also give a crispy edge. For the brownies, white sugar works best, but you can sub for brown if you prefer. I don’t recommend any liquid sweeteners here.

Egg. The brownie layer calls for one egg which you can sub for a vegan option like a flax egg or apple sauce. For the cookie layer, you need just one egg yolk. If you want to swap that out I suggest 2 tablespoons of greek yogurt.

Chocolate. I like semi-sweet chocolate chips and you can use either dutch process or regular cocoa powder for the brownies.

bite taken out of the gluten free brookie with melted chocolate

How to store and freeze

To store: Once prepared, these gluten free brookies will store for about 3-5 days. Allow them to cool completely before transferring to an air tight container. I store them at room temperature, but they’ll keep for longer in the fridge!

To freeze: allow to cool completely, then slice and place in a ziplock bag or wrap tightly in plastic wrap and place in a freezer safe container. Reheat in the oven at 300 until warm through the center and enjoy!

two gluten free brookies with a bite taken out to show texture

Try these desserts next!

  • Gluten Free Chocolate Cupcakes
  • Mini Brownie Bites
  • M&M Brownies
  • Chocolate Loaf Cake

If you want more recipes straight to your inbox, be sure to subscribe to my email list! As always, be sure to tag me on instagram so I can see your creation. Leave a comment and rating below if you try this recipe!

5 from 1 vote

Gluten Free Brookies

by: claire cary

These gluten free brookies combine two of the best desserts- a layer of fudgy gluten free brownies topped with a layer of thick chocolate chip cookies. They’re a rich, indulgent dessert that will impress all of your friends.
/ /
Prep: 20 minutes mins
Cook: 30 minutes mins
Total: 50 minutes mins
16

Equipment

  • Electric Mixer
  • 9×9 baking pan

Ingredients

Brownie Layer

  • ½ cup unsalted butter
  • ¾ cup semi sweet chocolate chips
  • ¾ cup white sugar
  • 1 teaspoon vanilla extract
  • 1 egg
  • ⅓ cup cocoa powder
  • ½ cup gluten free all purpose baking flour
  • ½ teaspoon salt

Cookie Layer

  • 6 tablespoons unsalted butter softened
  • ⅓ cup white sugar
  • ⅓ cup brown sugar
  • 1 teaspoon vanilla extract
  • 1 egg yolk
  • 1 cup gluten free all purpose baking flour
  • ¼ teaspoon baking powder
  • ¼ teaspoon baking soda
  • ½ teaspoon salt
  • ¾ cup semi sweet chocolate chips
US Customary – Metric

Instructions

  • Preheat the oven to 350 degrees Fahrenheit. Line a 9×9 baking pan with parchment paper and set aside.
  • To make the brownie layer: in a small bowl, add the butter and chocolate chips. Melt in the microwave in 30 second increments, stirring between each until fully melted.
  • In a second bowl, add the sugar, vanilla and egg. Use an electric mixer to beat for about 30 seconds. Add in the chocolate mixture and beat to combine. Fold in the cocoa, flour and salt. Mix until well combined. Transfer to the prepared baking pan and spread smoothly.
  • To make the cookie layer: Add the softened/room temperature butter, white sugar and brown sugar to a mixing bowl and beat with an electric mixer for about 30 seconds. Add in the egg yolk and vanilla and beat to combine.
  • Add in the flour (spoon and level to measure), baking powder, baking soda and salt. Mix to combine. Fold in the chocolate chips.
  • Divide the dough into about 4 large balls. Flatten each ball in your hand and place on top of the brownie layer, pressing into the corners of the pan. Take any leftover dough and press to fill in any gaps.
  • Top with extra chocolate chips if desired. Bake for 25-30 minutes or until the edges are just golden brown and the center looks set. Let cool fully in the pan, then slice and enjoy!

Notes

  • I used semi-sweet chocolate chips, which I recommend, but for a richer flavor, you can swap with dark. This works for both the cookie layer and brownie layer.
  •  
  • Be sure to let the brookies cool completely before slicing so they slice nice and clean and don’t crumble.
Serving: 1brookie / Calories: 306kcal / Carbohydrates: 36g / Protein: 3g / Fat: 18g / Saturated Fat: 10g / Polyunsaturated Fat: 1g / Monounsaturated Fat: 5g / Trans Fat: 0.4g / Cholesterol: 50mg / Sodium: 178mg / Potassium: 138mg / Fiber: 3g / Sugar: 25g / Vitamin A: 348IU / Calcium: 34mg / Iron: 2mg

Did you make this?

Mention @eatwithclarity or tag #eatwithclarity!

Related posts:

  1. Healthy Chocolate Chip Cookies
  2. Vegan Double Chocolate Chip Cookies
  3. Sweet Potato Oatmeal Cookies
  4. Gluten Free Cookie Cake
5 from 1 vote

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Comments

  1. Kaylee
    April 14, 2026

    Everything I bake from her site is 10/10. This is no different. ๐Ÿ™‚ I love that I can use the same recipe minus the flour to make it not GF also for those that don’t need it to be!5 stars

    Reply
    1. Claire Cary
      April 14, 2026

      Thank you, Kaylee! So happy to hear that!

      Reply
claire cary

Welcome,
I’m Claire

Eat With Clarity is a place for gluten free recipes that are just as good as the real thing. With plenty of vegan, vegetarian and paleo options, there is something here for everyone!


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