Preheat the oven to 350F and line an 8x8 inch pan with parchment paper. Melt the butter in a light colored saucepan over medium heat and keep cooking, swirling often, for 5 to 7 minutes until it foams, turns golden brown and smells nutty.
Remove the pan from the heat and immediately whisk in the miso paste until fully dissolved. Add the chopped dark chocolate and let it sit for 2 minutes, then stir until smooth and glossy.
Whisk the allulose into the chocolate mixture, then add the eggs one at a time, whisking well after each. Add the vanilla and beat for one full minute until the batter is thick and shiny.
Fold in the almond flour, cocoa powder and baking powder until no dry spots remain. Stir in the chocolate chips.
Spread the batter evenly into the pan and sprinkle the flaky sea salt over the top. Bake for 24 to 27 minutes, until the edges are set and a toothpick in the center comes out with moist crumbs.
Cool completely in the pan for at least 1 hour before slicing into 16 squares. The miso flavor deepens overnight, so these are even better the next day.