Preheat oven to 350°F and line or grease a 9x9 baking pan.
In a small saucepan, melt the butter and chocolate chips over low heat, stirring frequently until smooth. Set aside to cool and start on the red velvet cheesecake layer.
Make the red velvet cheesecake layer by beating the cream cheese in a stand mixer until smooth. Add the ⅓ cup sugar and beat until well combined.
Add the egg white, reserving the egg yolk for the brownie layer. Beat the egg in until smooth. Add the red velvet extract and vanilla extract and beat again. Set the cheesecake mixture aside and start the brownie layer.
Make the brownie layer by beating together the 3 large eggs + 1 egg yolk, brown sugar, ½ cup granulated sugar, and vanilla extract until smooth and frothy (about 2-3 minutes).
While the mixer is running on low, slowly pour in the cooled chocolate butter mixture and stir until well combined. Add the cocoa powder and salt and stir until well combined. Add the whole wheat pastry flour and stir until well combined.
Reserve about ¾ cup of the brownie batter, and pour the rest into the prepared baking pan. Spread with a spoon all the way to the edges, it will be thick! Top with the red velvet cheesecake layer, spreading it all the way to the edges. Add dollops of the reserved brownie batter to the top of the red velvet layer, then swirl gently with a butter knife.
Bake in the preheated oven for 30-35 minutes, or until a toothpick inserted into the center comes out mostly clean. Allow to cool, then remove from the pan, slice into 16 brownies, and serve! Store at room temperature for up to 3 days.
Notes
Storage Directions
Storing: Leftover red velvet cheesecake brownies can be kept in an airtight container at room temperature for up to 3 days or in the refrigerator for up to 5 days.
Freezing: For longer storage, you can also freeze the brownies. Once cooled completely to room temperature, transfer them to a freezer-safe container and store for up to 3 months. Defrost the brownies at room temperature for 30-60 minutes until thawed through.