Gluten Free Cheesecake Brownies

Gluten Free Cheesecake Brownies

Gluten free cheesecake brownies are the perfect mix of rich chocolate brownies and creamy cheesecake baked together easily in a muffin tin.

Cheesecake brownie bites on a black tray

Believe me when I tell you that I’ve tried really really hard to bake a classic cheesecake without a crust in either a muffin tin or an actual cookie. I’ve failed spectacularly, but I am determined to keep trying. These gluten free cheesecake brownies are an excellent consolation prize.

Here, we use a rich and fudgy chocolate brownie as the perfect sturdy base. Then, pour a classic cheesecake filling on top of each brownie base.

The cheesecake bakes just enough as the brownie batter sets, but not too much. I would never offer you overbaked cheesecake. That would be almost criminal.

Plus, cheesecake with brownies are a lot like Reese’s Peanut Butter Cups. Two great tastes that taste great together.

Gluten Free Cheesecake Brownie Bites, Step by Step

Two bite cheesecake brownies made one way…

If you would like to make small cheesecake brownies in a miniature muffin tin, the method calls for 3 layers of batter. First, add a base of brownie batter. Then, top with some cheesecake mixture, and finally more brownie batter.

When you bake these in a miniature muffin tin, they bake much faster. If you have a thick layer of brownie batter and a thin layer of cheesecake without a small topping of brownie batter, the cheesecake tends to overbake.

Cheesecake brownie cut in half on small white plate

Full-sized cheesecake brownies baked another way

When you make the cheesecake brownies in a standard 12-cup muffin tin, you don’t get the 2-bite effect of the miniatures. But you do get away with two layers of batter.

First, divide the brownie batter evenly among the prepared wells of the standard muffin tin. Smooth the tops with wet fingers.

Then, top with the cheesecake mixture. There’s no need to cover the cheesecake layer during baking with more brownie batter. They’ll bake perfectly as is.

A close u of a stack of cheesecake brownie bites on wooden surface

Ingredients and substitutions

I don’t have great news for making this cheesecake brownie recipe while avoiding additional common allergens.


There are ways that you could make the brownie layer without dairy. You could try replacing the butter with vegan butter (Melt and Miyoko’s Kitchen brands are best), or even Earth Balance buttery sticks. The milk can be nondairy.

But the cream cheese in the cheesecake layer stops us in our tracks. I have not ever found a dairy-free cream cheese that tastes like the “real” thing.


You might be able to replace each of the eggs in the brownie recipe with a “chia egg” (1 tablespoon ground white chia seeds + 1 tablespoon lukewarm water, mixed and allowed to gel). You might be able to replace the egg white with the brine from a can of chickpeas (called aquafaba).

But if you replace the egg in the cheesecake with a “chia egg,” I don’t expect that you’ll get the right texture. If you decide to give it a try, let us know how it turns out!


Cheesecake brownie on small white plate

Cheesecake Brownie whole and cut in half

Like this recipe?

Prep time: Cook time: Yield: 12 standard or 24 mini cupcakes


For the Brownie Batter
1 1/3 cups (187 g) all purpose gluten free flour (I used my Better Than Cup4Cup Blend)

1/2 teaspoon xanthan gum (omit if your blend already contains it)

2/3 cup (53 g) unsweetened cocoa powder (natural or Dutch-processed, but I prefer Dutch-processed)

1/4 teaspoon kosher salt

1/4 teaspoon baking soda

2/3 cup (133 g) granulated sugar

2/3 cup (145 g) packed light brown sugar

8 tablespoons (112 g) unsalted butter, melted and cooled

3 tablespoons (1 1/2 fluid ounces) milk (any kind), at room temperature

2 eggs (100 g, weighed out of shell) + 1 egg white (25 g) at room temperature, beaten

1 teaspoon pure vanilla extract

For the cheesecake batter
8 ounces cream cheese, at room temperature

1/2 cup (100 g) granulated sugar

1/8 teaspoon kosher salt

1 egg (50 g, weighed out of shell) at room temperature, beaten

1/2 teaspoon pure vanilla extract


  • Preheat your oven to 325°F. Grease a 24-cup miniature muffin pan or a standard 12-cup muffin tin, and set it aside.

  • Make the brownie batter. In a large bowl, place the flour blend, xanthan gum, cocoa powder, salt, baking soda, and granulated sugar, and whisk to combine well. Add the brown sugar and whisk again to combine, breaking up any lumps. Create a well in the center of the dry ingredients, and add the butter, milk, eggs and vanilla, mixing to combine well after each addition. The batter will be thick and glossy. Set the brownie batter aside.

  • Make the cheesecake batter. In a large bowl with a hand mixer (or the bowl of a stand mixer fitted with the paddle attachment), beat the cream cheese on medium speed until light and fluffy. Add the sugar, salt, egg and vanilla, beating well after each addition. The batter should be light and fluffy.

  • If you’re making miniatures, place about 1 tablespoon of the brownie batter in the bottom of each of the prepared muffin tins and shake the muffin tin back and forth vigorously until the batter in each cup is smooth and even on top. Place about 1 tablespoon of cheesecake batter on top of the brownie batter in each well and shake into an even layer again. Place about 2 teaspoons of brownie batter on top of the cheesecake layer, and smooth into an even layer with wet fingers. The top layer of brownie batter will not completely cover the cheesecake layer. Place the tin in the center of the preheated oven and bake until a toothpick inserted in the center comes out with a few moist crumbs attached, but no wet batter (about 15 minutes). Remove from the oven and allow to cool in the muffin tin for 10 minutes before transferring to a wire rack to cool completely.

  • If you’re making standard size cupcakes, divide the brownie batter evenly among the prepared wells of your standard 12-cup muffin tin. With wet fingers, spread the batter into an even layer in each well. Transfer the cheesecake batter to a measuring cup with a pour spout, and pour just enough of the cheesecake mixture over the top of each brownie batter layer to cover the brownie batter completely. There should be just enough cheesecake batter for each of the 12 cupcakes. Place in the center of the preheated oven and bake for 20 to 22 minutes, or until the cheesecake layer is mostly set, but wiggles gently when moved back and forth. Remove from the oven and allow to cool in the muffin tin for 10 minutes before transferring to a wire rack to cool completely.


Comments are closed.

  • Loretta K
    April 27, 2015 at 7:21 PM

    Nicole, do you think I could use my store bought GF brownie mix (Better Batter product) in place of the brownie recipe? Just thinkin…

    • May 1, 2015 at 3:37 PM

      I don’t think a straight-up brownie batter would do well in mini muffins, no, Loretta.

  • Marilyn daigre
    April 27, 2015 at 2:16 PM

    Wow! the sound better then the gf caramel cheesecake bites I just finished making. Will have to try these next week.

  • Patricia van Dyke
    April 27, 2015 at 1:33 PM

    I was wondering if you know the nutritional info on these cheesecake brownie bites? I love gluten free recipes, but I also watch what I’m taking in. Thank you

    • May 1, 2015 at 3:38 PM

      Patricia, I don’t provide nutritional information, no. But feel free to plug in the ingredients into an online calculator and you’ll find all the information you need!

  • youngbaker2002
    April 25, 2015 at 12:23 PM

    We’re going to make these today! we went to Kohl’s yesterday to get our babycakes doughnut maker and it was out of stalk! :( We are now waiting for it to be delivered so we can make some hostess doughnuts. thanks for all the great recipes! -Mena

    • youngbaker2002
      April 25, 2015 at 1:00 PM

      Oh and I was wondering if you ever had a problem with yours sticking? Corrie said that she did. Should i put liners in to prevent that from happening? What do you recommend greasing the wells with? thanks again.

      • youngbaker2002
        April 25, 2015 at 6:35 PM

        A couple of them did stick a little but over all it went pretty well. i greased the wells with shortening. they taste sooo good! thanks!

  • arnab
    April 25, 2015 at 10:02 AM

    These are in the oven. I used the mini muffin tins, and the amount of each batter in each as per the directions, but it only made 24. No way would this make 40. And I made sure to measure each batter to make sure they would each be the right size. Sure hope they do not stick. I used cooking spray on teflon muffin tins.

    • April 26, 2015 at 6:40 AM

      Arnab, I made this recipe 3 times and got 40 each time. If I had used all of the batter in just 24 muffins they would have significantly overflowed the wells during baking. It sounds like you have rather large mini muffin wells.

    • nvcrisman
      May 1, 2015 at 3:31 PM

      I had this exact same issue, and I barely had enough brownie batter. I don’t know how one would have gotten 40 tablespoons out of the brownie batter recipe. Mine came out with shelves essentially on top, tasted great, just not as pretty.

      • May 1, 2015 at 3:39 PM

        Again, nvcrisman, it sounds like a difference in the size of the muffin wells. Glad the recipe turned out tasting good, though!

  • Corrie
    April 24, 2015 at 9:02 PM

    Use Cupcake Liners I
    greased and they STUCK like CRAZY and i have a Pile of YUMMY MUSH!!!!

    • April 26, 2015 at 6:39 AM

      Hi, Corrie, I’m sorry your cupcakes stuck to your pan, but that isn’t a function of the recipe, but of either the way you greased the wells or the pan itself. Next time, try using cooking oil spray, which gets in all the crevices most effectively.

  • Jennifer S.
    April 24, 2015 at 9:24 AM


  • Lucy
    April 24, 2015 at 9:09 AM

    Yum! You’re sooooo right Linda :)
    Chaperoning tweens for 2 days, wish me luck :)

    • April 26, 2015 at 6:40 AM

      Good luck, Lucy!!

  • Linda Vanderbaan
    April 24, 2015 at 8:23 AM


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