Preheat oven to 325°F. Lightly grease two mini muffin tins.
In a medium microwave-safe bowl, melt chocolate and butter in 20 second increments, stirring after each. Add the sugar, whisking to combine. Add in the eggs, whisking until smooth and then whisk in vanilla. Using a spoon, stir in the flour, instant coffee, and salt until combined. Fold in baking chips.
Spoon the batter into the prepared pans (you should have about 20 bites). Top each bite with a pretzel, gently pressing it down. Bake one pan at a time for 13-15 minutes each.
Cool bites in pans on a wire rack for 30 minutes. Sprinkle with sea salt and dig in!