Preheat the oven to 350° F. Line 12 muffin tins with paper liners.
In a bowl, whisk together the eggs, maple syrup, milk, and vanilla until combined. Add the flour, cocoa powder, instant coffee powder, baking powder, baking soda, and salt. Mix until just combined. Stir in the mini chocolate chips and melted butter.
Divide the batter evenly among the prepared pan. Bake for 22-25 minutes.
Meanwhile, make the fudge. Melt the chocolate and milk together over low heat, stirring often until smooth.
Using a paring knife, cut a cone-shaped piece from the center of each muffin. Fill the hole with chocolate fudge and replace the top.
