This is a stack of three brownies on a white counter and white background. The brownies have a cheesecake layer.
Gluten-free cheesecake brownies are a fudgey chocolate brownie topped with a cheesecake swirl. They’re flourless, super rich, and indulgent!

Gluten-free cheesecake brownies have been my latest obsession. If you like brownies and you like cheesecake you are going to throughly enjoy this little love baby recipe.

These fudgey chocolate brownies are swirled with cream cheese. The creamy cheesecake layer is the perfect compliment to the deep, rich chocolate brownie!

This is a side image of a brownie with a cheesecake top layer and a bite taken out. The brownie sits on a white piece of parchment paper and more brownies are blurred in the background.

Ingredients for gluten-free cheesecake brownies:

Gluten-Free Brownie bottom:

  • Chocolate Chips: they’re going to be the chocolatey base of these brownies!
  • Coconut Sugar: this is what we’re going to use to sweeten the brownies. It adds a rich, caramel depth to the brownies that are so delish!
  • Agave Nectar: a little extra sweetness. If you don’t have agave nectar or don’t like it, you can sub in honey or maple syrup instead.
  • Eggs: just a couple eggs and we’re adding in an extra yolk to bump up the fudge factor of these brownies.
  • Vanilla: just a splash!
  • Blanched Almond Flour: this is going to give the brownies some structure. I love super-fine blanched almond flour because it makes for a smoother dessert compared to an almond meal or something with more texture to it.
  • Cocoa Powder: this will give an extra layer of richness to these brownies!
  • Salt: just a bit.

Cheesecake layer:

  • Cream Cheese: this is kinda necessary if you’re making cheesecake brownies! I always go for full fat cream cheese!
  • Agave Nectar: to sweeten up the cream cheese. You can also sub in honey or maple syrup if you don’t have or like agave nectar.
  • Egg: will help the cream cheese layer set when we bake it.
  • Vanilla: to give the cream cheese layer some vanilla vibes.

How to make gluten free chocolate brownies with a cream cheese swirl:

It’s so simple! It’s a two step process and I think my favorite step is when the swirl action happens…

Make the brownie layer. Whisk together the melted chocolate, coconut sugar, agave, eggs and egg yolk, and vanilla. 

Once smooth, add the almond flour, cocoa powder, and salt. Whisk until combined and set aside. 

Make the cheesecake layer. In a separate, medium bowl, use a clean whisk to cream together the room temperature cream cheese, agave, egg, and vanilla until smooth. 

Add the layers to the pan. Line an 8×8 square pan with parchment paper so that it is draped over two sides. 

Pour ⅔ of the brownie batter into the pan and use a rubber spatula to spread it into the edges and corners. 

Pour the cheesecake batter on top of the brownie layer and spread it out. 

Finally, scoop the remaining brownie batter on top of the cheesecake layer, putting them in little dollops across the top.

Swirling happiness. Use a toothpick or chopstick to create swirls in the brownie dollops and cheesecake layer. 

Bake. Bake for 30 minutes. Remove the brownies from the oven and allow to cool for 15 minutes before cutting into them.

This is an overhead image of brownies with a cheesecake swirl. The brownies are cut into squares and sit on a white piece of parchment paper on a white counter. A knife is in the bottom corner of the image.

How to store these gluten-free cheesecake brownies:

You can leave them out on at room temperature overnight in a sealed container. They’ll keep for about 5 days in the fridge or 3 months in the freezer.

Defrost in the fridge overnight and warm in the microwave or oven until heated through.

Fun toppings to add to your cheesecake brownies:

Chopped pecans would add a really fun nutty element to these brownies. You could even add some strawberry chia jam or a caramel drizzle!

More flourless brownies recipes:

This is a stack of three brownies on a white counter and white background. The brownies have a cheesecake layer.

Fudgey Gluten-Free Cheesecake Brownies

  • Author: Lindsay Grimes Freedman
  • Prep Time: 15 min
  • Cook Time: 30 min
  • Total Time: 45 min
  • Yield: 16 brownies 1x
  • Category: dessert
  • Method: oven
  • Cuisine: brownies
  • Diet: Gluten Free
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These flourless cheesecake brownies are a fudgey chocolate brownie topped with a cheesecake swirl. Super indulgent and naturally gluten free!



Brownie layer:

  • 1 ½ cup chocolate chips, melted
  • ½ cup coconut sugar
  • 4 tablespoons agave nectar
  • 2 eggs + 1 egg yolk
  • 1 teaspoon vanilla
  • 1 cup blanched almond flour
  • 1/4 cup cocoa powder
  • ½ teaspoon salt

Cheesecake layer:

  • 1 (8 oz) package cream cheese, room temperature
  • 3 tablespoons agave nectar
  • 1 egg
  • ½ teaspoon vanilla


  1. Preheat oven to 350F.



  • Serving Size: 1 brownie
  • Calories: 219
  • Sugar: 22.2g
  • Sodium: 132mg
  • Fat: 12.3g
  • Saturated Fat: 6.6g
  • Unsaturated Fat: 0g
  • Trans Fat: 0g
  • Carbohydrates: 26.6g
  • Fiber: 2.1g
  • Protein: 4.6g
  • Cholesterol: 57mg

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