Preheat your oven to 325°F. Spray a 9x9-inch baking pan with nonstick cooking spray and line it with parchment paper, leaving a 2-inch overhang for easy removal later.
In a medium bowl, whisk 1 whole egg and 1 egg yolk (reserve the white). Add 1/4 cup water, raw honey, and 1 teaspoon of vanilla extract. Stir until everything is combined.
In a separate large bowl, whisk together the almond flour, cocoa powder, kosher salt, and baking soda. Gently fold the wet mixture into the dry ingredients until just combined.
Stir in semisweet chocolate chips, ensuring they're evenly distributed. Pour the batter into your prepared pan, smoothing out the top with a spatula.
In another bowl, microwave the cream cheese until softened, then mix in sugar, reserved egg white, and the remaining 1 teaspoon of vanilla extract until smooth.
Gently pour the cream cheese mixture over the brownie batter, spreading it evenly. Use a toothpick or knife to swirl the two layers together for a marbled effect.
Bake for approximately 30 minutes, or until a toothpick inserted in the center comes out clean.
Allow the brownies to cool completely (at least 30 minutes) before slicing into 12 bars. Serve and enjoy!