Preheat the oven to 350°F and line a baking sheet with parchment paper.
Stir almond flour, coconut flour, powdered allulose, baking powder, and salt in a bowl.
Add softened butter, egg, and vanilla extract. Mix until the dough is thick and smooth.
Scoop 12 cookies onto the baking sheet, flatten slightly, and bake for 9 to 11 minutes until the edges are set.
Cook allulose, butter, and heavy cream in a small saucepan over medium-low heat for 4 to 6 minutes, stirring until amber and glossy. Stir in vanilla extract.
Spoon the caramel over the warm cookies and press keto pretzel pieces into the tops.
Sprinkle with flaky sea salt and cool completely before serving.