Blend the cottage cheese in a small blender or food processor until completely smooth.
In a large bowl, beat the butter and sweetener until creamy. Add the blended cottage cheese, egg, and vanilla, and beat until smooth.
In a separate bowl, whisk together the almond flour, cocoa powder, baking soda, and salt, breaking up any cocoa lumps.
Stir the dry ingredients into the wet ingredients until a thick, fudgy dough forms. Fold in the chocolate chips and chill the dough for 20 minutes.
Preheat the oven to 350°F and line a baking sheet with parchment paper. Scoop the dough into 1 1/2 tbsp balls and flatten each one to about 1/2 inch thick.
Bake for 11 to 12 minutes. The centers will look slightly soft, which keeps them fudgy once cooled.
Let the cookies cool on the baking sheet for 15 minutes before moving them to a wire rack.