Preheat your oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners. In a medium bowl, whisk together the coconut flour, Swerve Sweetener, cocoa powder, whey protein powder, baking powder, and salt until no lumps remain.
In a separate large bowl, whisk the eggs until well combined. Gradually whisk in the melted butter and vanilla extract until smooth.
Add the dry ingredients to the wet ingredients in three additions, mixing well after each addition until just combined. The batter will be very thick.
Stir in the coffee or water, adding more if needed, until the batter reaches a thick but pourable consistency. Do not overmix.
Divide the batter evenly among the 12 prepared muffin cups, filling each about two-thirds full.
Bake for 20-25 minutes, or until a wooden skewer inserted into the center of a cupcake comes out clean. Let the cupcakes cool in the muffin tin for 5 minutes before transferring them to a wire rack to cool completely. Frost once cooled, if desired.