Prep your pan and oven. Heat the oven to 350°F (175°C). Line an 8-inch square pan with parchment, leaving overhang for easy lifting.
Lightly grease the parchment.
Melt the chocolate. In a microwave-safe bowl, melt the dark chocolate chips with the coconut oil in 20–30 second bursts, stirring between each. Set aside to cool slightly so it doesn’t scramble the eggs.
Whisk the wet ingredients. In a mixing bowl, whisk eggs, Greek yogurt, applesauce, maple syrup, and vanilla until smooth and glossy.
Combine the dry ingredients. In another bowl, whisk protein powder, cocoa powder, almond flour, baking powder, and salt. Break up any clumps—this matters for a smooth batter.
Bring it together. Pour the melted chocolate mixture into the wet ingredients and whisk to combine.
Add the dry ingredients to the bowl and fold gently with a spatula until no dry streaks remain. The batter will be thick and shiny.
Add-ins for texture. Fold in a handful of extra chocolate chips or chopped nuts if you like. Don’t overmix.
Spread and smooth. Transfer the batter to the lined pan.
Use a spatula to level the top. For a bakery finish, sprinkle a few chips on top and a pinch of flaky salt.
Bake. Bake for 18–24 minutes, checking at 18. You want set edges and a slightly soft center.
A toothpick should come out with moist crumbs, not wet batter.
Cool completely. Let the pan cool on a rack for at least 30–45 minutes. Lift the brownies out using the parchment. Cooling helps them set to that fudgy texture.
Slice and serve. Use a sharp knife, wiping between cuts for clean edges.
Aim for 9–12 squares, depending on your preferred portion size.