Add the dark chocolate chips along with the butter to a small saucepan. Set over low heat and stir until completely melted and smooth. Remove from the heat and let cool while you go on to the next steps.
In a small bowl, sift the flour, cocoa powder, and salt together. Set aside.
In the bowl of a stand mixer fitted with the whisk attachment, or in a large mixing bowl if using a hand mixer, beat the eggs and sugar together until the mixture is pale and thick (2 to 3 minutes.) Turn the speed down to low and pour the reserved melted butter and chocolate mixture into the mixing bowl, stirring just until combined. Using a spatula, fold the flour and cocoa mixture into the batter until just a few streaks of flour remain.
Divide the batter between the cups of the prepared mini muffin pan. (You can use a 1½ tbsp (7 ml/medium) cookie scoop to do this swiftly.) Bake for 10 to 11 minutes. Do not overbake: Start monitoring the brownie bites at the 9-minute mark: you want to take them out of the oven right when the tops dry up. At 9 minutes, they should be puffed but still look a bit wet in the center. From there, they’ll set within a minute or two. Transfer the pan to a rack and let cool completely.
For the Salted Fudge Frosting: Add all the ingredients to a medium saucepan. Set over medium-low heat and stir until the chocolate and butter are melted and the mixture is smooth. Transfer to a large, shallow bowl, or to a large container. Refrigerate about 2 hours, or until the frosting is thick. (Whisking the frosting once or twice during that time will help it cool faster.)
SERVING: Transfer the salted fudge frosting to a piping bag set with a large, round tip. Pipe a generous amount of frosting over each brownie bite. Alternatively, you can use a butter knife or an icing spatula to spread the frosting over the brownie bites. Sprinkle with additional fleur de sel or flaky sea salt, if desired.
Always serve the brownie bites at room temperature.
STORAGE: Store the frosted brownie bites in an airtight container at room temperature for up to 2 days, refrigerate for up to 1 week, or freeze for up to 1 month. Make sure to bring the brownie bites to room temperature before serving (30 minutes if refrigerated, 60 to 90 minutes if frozen.)
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