Matcha Brownie with Cheesecake Swirl

Mar 17, 2022

This is the best gluten free matcha brownie recipe – A new take on the cheesecake brownie you didn’t know you needed. Gluten free dark chocolate cheesecake brownies are rich and fudgy with a picturesque cream cheese and matcha swirl.

Even with the picture perfect swirl, they’re easy to whip up, and make a delicious healthy treat that are low in sugar, gluten free and can be made dairy free too. Loaded with antioxidants from the matcha and dark chocolate this matcha brownie recipe makes for a healthy and decadent treat!

What You’ll Need For The Best Matcha Brownies

  • Unsalted Butter
  • Dark Chocolate Chips
  • Maple Sugar
  • Matcha Powder, culinary grade
  • Cream Cheese
  • Quality Cocoa Powder
  • Almond Flour, super fine
  • Pasture Raised Eggs
  • Vanilla Extract

See below for possible substitutions.  

How To Make A Paleo Matcha Brownie 

There are a few different steps to making this recipe, but don’t get intimidated, it’s so easy!

Essentially there are two main steps: First, make the brownie layer by melting together butter and chocolate. YUM. Stir sugar into the melted chocolate mixture, along with vanilla, salt and almond flour.

Secondly, make the cheesecake layer. Whip together the cream cheese, egg and vanilla until silky smooth. Reserve half the mixture in a separate bowl then whisk in the matcha powder to the mixture so that half the cream cheese topping is plain and half is green.

Then put them together, swirl and bake in the oven. You’ll want to dollop spoonfuls of plain and matcha cheesecake batter, rotating the colors, then making swirls with a toothpick or pairing knife for the beautiful swirl.

See below for the step by step details.

Ingredient & Substitution Suggestions for Your Matcha Brownie

Matcha Powder, culinary grade: If you’re new to matcha, it’s a green tea powder known for its high antioxidant content. Whether or not you’re a fan, I’m certain you’ll love these brownies.

The key is good quality matcha powder for a fresh flavor. There’s ceremonial grade which is a bit more delicate in flavor, so look for culinary grade, which is more appropriate for cooking. I used this culinary grade matcha.

Cream Cheese: You can use full fat dairy cream cheese or dairy free cream cheese. I’ve tested both for you and either way it’s delicious! If you choose to use dairy cream cheese, I’d recommend using full-fat, organic and pasture raised.  If you choose to use dairy-free cream cheese, my preference is Kite Hill plain cream cheese.

Cocoa Powder:  Cocoa powder can vary based on quality. There’s a difference between hot chocolate mix and cacao powder. Look for organic, unsweetened baking cocoa powder for the best, rich chocolatey flavor. This one is my favorite. You can use cacao powder if you want, however it will lend a slightly more bitter flavor.

Dark Chocolate Chips: The higher the percentage of chocolate, the more antioxidant content it has and the lower sugar it contains. These brownies have a rich decadent chocolate flavor from dark chocolate around 85%. Again, look for an organic dark chocolate like Endangered Species chocolate bar or Pascha dark chocolate chips.

Maple Sugar:  You can substitute any granulated sugar in this recipe, but here’s why I recommend Maple Sugar. It’s unrefined, which means it still retains some nutrients.

You can use coconut sugar, which is another common unrefined sugar, but it makes the cheesecake swirl a slight brown color and doesn’t taste as sweet as maple sugar.  And it lends the perfect amount of sweetness and light maple flavor. If you haven’t tried it, I highly recommend giving it a try. You can find it at Thrive Market. You can use this link to get 40% off your first purchase AND a free gift!

Almond Flour:  Almond flour binds the brownie together, gives it a fudgy texture and keeps it gluten free. Some are gritty and make the brownie more crumbly so look for super fine, blanched flour like Bob’s Red Mill.

Butter:  Same as the cream cheese, look for organic, pasture raised butter.

Pasture Raised Eggs:  Again… organic and pasture raised eggs are recommended for this recipe. Pasture raised and organic provides the most nutrients like vitamin B, choline, omega-3’s and antioxidants. And just because it’s a dessert, don’t skimp on ingredients. Desserts can be nutrient dense too!

Sea Salt:  Salt makes food taste more like itself, which means it enhances the rich chocolate goodness.


What Makes These Matcha Brownies Healthy?

These brownies are great for many people with food sensitivities.

They’re gluten free, grain free, refined sugar free, and there’s the option to make them dairy free as well.  Because they’re “free” of all these foods that are generally irritating to most people makes them generally better for gut health and hormone health.

BUT, that’s not to say they lack in any flavor! In fact, the most flavorful food often provides the most beneficial nutrients in compounds called phytochemicals, aka antioxidants.

These phytochemicals/antioxidants reduce inflammation and damage in the body.

And guess what!? Flavor follows phytochemicals; meaning the most flavorful foods have more phytochemicals with more health supporting properties. So why are these fudgy matcha brownies healthy?

  • Chocolate is a rich source of antioxidants.
  • Matcha is an exceptional source of another type of antioxidants.
  • Quality organic, pasture raised dairy and eggs also provide beneficial phytochemicals.

Moreover, these matcha brownies use unrefined sugar, which means you can benefit from the nutrients that remain intact.

AND because they use less sugar than most brownie recipes they’re better for blood sugar and hormone balance and gut health.

Above all, these healthy matcha brownies are delicious, but you can feel good about nourishing yourself when you eat them too.

Download the free Sweet Treats eCookbook with 7 of my favorite lightly sweetened desserts to satisfy cravings while reducing inflammation.

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All recipes are gluten, dairy, grain and refined sugar free!

How To Store Your Matcha Brownies

If you’re going to use dairy cream cheese you’ll want to store these in the refrigerator in an air tight container. Even if you use dairy free cream cheese, I’d still recommend keeping them in the fridge. Keeping them chilled will keep the cheesecake layer more solid and the brownie fudgy and moist. They’ll keep for 3-4 days refrigerated.  

Other Recipes You’ll Love

If you want other dessert recipes that are low in sugar for your health needs, but full of flavor and decadence, you’ll definitely want to check out these recipes too!

Chocolate Raspberry Parfait

Chocolate Coconut Pecan Truffles

Ginger Spice Bites

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Matcha Brownie

Matcha Brownies with Cheesecake Swirl

  • Prep Time: 15 minutes
  • Cook Time: 24 minutes
  • Total Time: 39 minutes
  • Yield: 16 brownies 1x
  • Category: Dessert
  • Cuisine: Gluten Free, Paleo


Fudgy brownies with a layer of cheesecake and a think ribbon of matcha… You'll be surprised how much you love this healthy treat.


Units Scale


  • 1/2 cup (1 stick) unsalted butter (or ghee)
  • 1/2 cup (3 oz) chocolate chips 85% (I like Pascha)
  • 1/4 cup maple sugar
  • 3 large eggs
  • 1 teaspoon vanilla extract
  • 1/2 teaspoon sea salt
  • 1/4 cup cocoa powder
  • 1/2 cup super-fine almond flour

Cheesecake Layer

  • 8 oz room temperature cream cheese (dairy free or diary) (I like Kite Hill plain almond milk cream cheese)
  • 1 large egg
  • 3 tablespoons maple sugar
  • 1 teaspoon vanilla extract
  • 1 tablespoon culinary matcha powder


  1. Preheat your oven to 350 degrees with the rack on the middle shelf. Prepare an 8×8 metal pan by greasing the edges with butter and line the bottom with parchment paper allowing extra to extending over the sides.
  2. Place a heat proof glass bowl over a small pot of simmering water. Add the butter and chocolate chips in the bowl allowing the heat to gently for about 5 minutes to melt the two together. Once the butter has melted, stir until combined and set aside to cool.
  3. While the chocolate cools make the cheesecake layer. Add all the ingredients to a medium bowl, except for the matcha. Using a hand mixer (or a stand mixer), whisk until silky smooth.
  4. Scoop approximately half of the cream cheese mixture into a small bowl and set aside. Add the matcha to the remaining cream cheese mixture and mix again until fully combined, scraping down the sides as needed. Set this bowl aside as well as you finish the brownie mixture.
  5. In the cooled chocolate mixture, whisk the eggs and sugar until fully combined. Add the salt, cocoa powder, almond flour and mix until smooth.
  6. Pour all the brownie mix, except for approximately 3 tablespoons, into the prepared pan. Add 1-2 tablespoons of water to the remaining brownie mix to thin it out to a similar consistency as the cheesecake layer.
  7. Gather both bowls of cheesecake mix and a spoon. Starting with the matcha, drop large dollops on top of the brownie layer in a scattered pattern. Repeat with the plain cheesecake mixture, dropping large dollops in a scattered pattern between the matcha. Finally, repeat with the remaining diluted brownie mix.
  8. Gently drag a skewer or pairing knife, through the cheesecake layer in big swirls to make the marbled design on top. Don't over swirl on this step.
  9. Bake for 20-22 minutes, or until the top is set or a toothpick inserted into the middle comes out clean. Allow the brownies to cool fully before slicing into 16 brownies. Store in an air tight container for up to 3 days in the refrigerator. Enjoy!

Keywords: Chocolate, Dessert, Gluten Free, Paleo

  Make this matcha brownie recipe asap and let me know how much you love it by tagging me on Instagram @alannadesalvonutrition

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