Preheat your oven to 350°F and line an 8x8 inch baking pan with parchment paper, allowing some overhang for easy removal. While the oven heats, measure out all your ingredients and bring the eggs and cream cheese to room temperature—this ensures the chocolate won't seize when you add the eggs, and the cream cheese will swirl smoothly without lumps. Room temperature ingredients also mix more evenly, giving you a better final texture.
Combine the baking chocolate and butter in a heatproof bowl over gently simmering water (or use a microwave in 30-second intervals), stirring until completely smooth. Let cool for 5 minutes—this prevents the eggs from cooking when added. Stir in the sugar substitute until fully dissolved, then add the vanilla, red food coloring, and vinegar. The vinegar reacts with the baking soda to enhance the red velvet flavor and create a subtle tang.
Add the eggs one at a time to the chocolate mixture, stirring well after each addition to ensure they're fully incorporated before adding the next—this creates a silky, well-emulsified batter. In a separate small bowl, whisk together the almond flour, baking powder, and salt. Fold this dry mixture into the chocolate batter gently but thoroughly until no streaks remain. I find that folding rather than vigorously stirring helps keep the batter light and prevents overdeveloping gluten from the almond flour.
While the brownie batter rests, combine the softened cream cheese, sugar substitute, egg, vanilla, and vinegar in a separate bowl. Beat or whisk until completely smooth and lump-free—any lumps will remain visible in the final brownies. This topping will create the signature red velvet cheesecake swirl that makes these brownies special.
Pour the chocolate brownie batter from Step 3 into your prepared pan and spread evenly. Spoon the cream cheese mixture from Step 4 over the top in dollops, then use a knife or skewer to swirl through both layers in a figure-eight or crosshatch pattern, creating those beautiful red velvet ribbons. Bake for 20-35 minutes until the center just barely jiggles when you gently shake the pan—this indicates perfect fudgy doneness. The brownies will continue to set as they cool, so don't overbake.
Remove the pan from the oven and let the brownies cool in the pan for 10 minutes—this allows the structure to set enough to cut cleanly. Transfer to the refrigerator for at least 30 minutes before cutting. I like to chill them longer (1-2 hours) because the cold makes both the fudgy brownie and creamy cheese layer more defined, and the flavors meld beautifully. Cut into squares and store in an airtight container in the refrigerator.