Preheat your oven to 325°F and line a 9x9 inch baking dish with parchment paper, leaving some overhang on the sides for easy removal later. This setup ensures even baking and makes it simple to lift the cooled brownies out for cutting.
In a large mixing bowl, beat the room-temperature eggs with coconut sugar on high speed for 3-5 minutes until the mixture is thick, pale, and has roughly tripled in volume. This aerating step is crucial—it incorporates air into the batter, which helps the brownies achieve a fudgy yet slightly risen texture rather than being dense and flat.
In a separate small bowl, whisk together the almond flour, coconut flour, dark cocoa powder, and sea salt. Pour the coffee and vanilla into the egg mixture, then gently fold in the dry ingredient mixture until just combined, being careful not to overmix and deflate the aerated eggs. I find that folding by hand with a spatula rather than using the mixer helps preserve all that air you just incorporated.
Place 1 cup of chocolate chips and the melted coconut oil (cooled to room temperature) in a microwave-safe bowl. Microwave in 30-second intervals, stirring between each burst, until completely smooth and melted—this usually takes 60-90 seconds total depending on your microwave. Letting it cool before adding to the batter prevents the eggs from scrambling.
Pour the melted chocolate mixture into the batter and fold gently until no streaks remain, then fold in the remaining 1/4 cup of chocolate chips. Pour the complete batter into your prepared baking dish and spread it evenly with a spatula. I like to tap the pan gently on the counter once or twice to release any large air bubbles.
Bake at 325°F for 35-40 minutes until a toothpick inserted in the center comes out with just a few moist crumbs (they should not be wet batter). Remove from the oven and let the brownies cool completely in the pan, which takes about 30 minutes—this allows them to set properly so they cut into clean squares. Once cooled, use the parchment overhang to lift the entire brownies out and cut into squares.