Preheat the oven to 350 degrees F (175 degrees C). Line a square 9-inch baking pan with foil. Grease foil with cooking spray.

Beat cream cheese and sugar in a large mixing bowl until smooth and light. Add egg; beat until smooth. Set cheesecake layer aside.

Beat sugar and butter in a large bowl until fluffy. Add eggs one at a time, beating well after each addition. Beat in cocoa powder and coffee granules.

Sift flour, baking powder, and salt together onto a large piece of waxed paper. Add all at once to the chocolate mixture; stir until blended. Add vanilla extract. Set 1/3 cup of batter aside in a small bowl; stir in milk. Fold chocolate chips and almonds into the remaining batter.

Pour larger portion of batter into the prepared pan. Carefully spread cream cheese mixture on top. Drop teaspoonfuls of reserved batter over the cream cheese layer. Run a clean knife through the batter and cheesecake to create swirls.

Bake in the preheated oven until cheesecake is set and a toothpick inserted halfway to the center of the pan comes out clean, 30 to 35 minutes. Cool on a wire rack.