Make the caramel first: melt butter in a small saucepan, add powdered allulose, and cook 3 to 4 minutes until deep amber. Carefully whisk in the heavy cream and simmer 2 minutes.
Remove from heat and stir in the vanilla and flaky sea salt. Pour into a small bowl and chill 30 minutes until thickened to a spoonable consistency.
Preheat oven to 350F and line a 9x9 pan with parchment paper.
Whisk together the melted butter, melted chocolate, powdered allulose, eggs, and vanilla until smooth and glossy.
Fold in the almond flour, cocoa powder, and salt until a thick batter forms. Spread half into the prepared pan.
Dollop most of the caramel evenly across the batter, leaving a small amount for drizzling. Top with the remaining brownie batter and smooth carefully.
Drizzle the reserved caramel on top and swirl gently. Bake for 24 to 27 minutes until set around the edges but still fudgy in the center.
Cool completely, then sprinkle with flaky sea salt and slice into squares.