Preheat your oven to 350°F (175°C) and line an 8x8-inch baking pan with parchment paper, leaving a slight overhang for easy removal.
In a large mixing bowl, whisk together the almond flour, protein powder, cocoa powder, baking powder, and sea salt until no lumps remain.
In a separate medium bowl, combine the almond butter, eggs, sugar-free maple syrup, and vanilla extract. Whisk vigorously until the mixture is completely smooth and emulsified.
Pour the wet ingredients into the dry ingredient bowl. Use a silicone spatula to fold the mixtures together until just combined. Do not overmix, as this can make the protein powder tough.
Gently fold in 2 tablespoons of the mini chocolate chips.
Transfer the batter into the prepared baking pan. Use the back of a spoon or a wet spatula to spread it evenly into the corners, as the batter will be very thick.
Sprinkle the remaining chocolate chips evenly over the surface of the batter.
Bake for 18 to 22 minutes. The brownies are done when the edges are set but the center still appears slightly soft; a toothpick inserted should come out with a few moist crumbs.
Remove from the oven and allow the brownies to cool completely in the pan for at least 30 minutes. This cooling period is critical for the protein structure to set.
Lift the brownies out using the parchment overhang and slice into 9 even squares.