Preheat oven to 350°F. Line a 12-cup mini muffin tin with mini cupcake liners, or grease generously.
Melt the butter and sugar-free dark chocolate together in a microwave-safe bowl in 30-second intervals, stirring between each, until completely smooth. Let cool for 3 minutes.
Whisk the powdered erythritol, eggs, and vanilla extract into the chocolate mixture until smooth and glossy. Add the almond flour, unsweetened cocoa powder, and sea salt, then fold with a spatula until just combined. The batter should be thick and fudgy.
Divide the batter evenly among the 12 mini muffin cups, filling each nearly to the top. Sprinkle a few flakes of sea salt on top of each.
Bake for 12 to 14 minutes. The tops should look set and slightly cracked, but a toothpick inserted in the center should come out with moist crumbs, not wet batter. Do not overbake - this is the key to fudgy centers.
Let the brownie bites cool in the tin for 10 minutes before removing. They will firm up as they cool. Serve at room temperature for the most fudgy texture.
