Preheat the oven to 350°F. Line the bottom and sides of a 9-by-9-inch baking pan with foil, leaving an overhang on the ends.
Prepare cheesecake layer: In a small bowl, beat cream cheese and sugar until smooth. Add 1 egg and flour, and beat until blended; set aside.
In a medium bowl, whisk together flour, pumpkin pie spice, baking soda, and salt; set aside.
With an electric mixer, cream butter and sugar on medium-high speed until smooth; beat in 1 egg and vanilla until combined. Beat in pumpkin puree (mixture may appear curdled). Reduce speed to low, and mix in dry ingredients until just combined. Stir in 1 cup chocolate chips.
Spread batter evenly in the prepared pan. Spread the cream cheese mixture over the pumpkin batter. Sprinkle with ½ cup chocolate chips.
Bake until the edges begin to pull away from the sides of the pan and the cheesecake is set, about 45 minutes. Cool completely in the pan.
Lift bars from the pan (using foil as an aid). Peel off the foil and use a serrated knife to cut into 16 squares.