Mix the cream cheese, powdered allulose, and vanilla until smooth. Spoon 12 small mounds onto a parchment-lined plate and freeze for 30 minutes.
Heat the oven to 350°F and line two baking sheets with parchment paper. Whisk the almond flour, cocoa powder, baking soda, and salt together.
Beat the softened butter and brown monk fruit sweetener until creamy. Beat in the egg and vanilla, then stir in the dry ingredients and chocolate chips to make a thick dough.
Divide the dough into 12 portions. Flatten each portion, place one frozen cheesecake mound in the center, and gently wrap the dough around it so the cream cheese is fully enclosed.
Arrange the cookies several inches apart and flatten the tops very slightly. Bake for 11 to 13 minutes, until the edges are set and the centers still look soft.
Cool on the baking sheets for 10 minutes so the cookies can firm up without losing their fudgy centers.
Refrigerate for 20 minutes for a thicker cheesecake center, or serve slightly warm for a softer filling.