Preheat oven to 350°. Line bottom and sides of a 9-by-9-inch baking pan with foil, leaving an overhang on 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 prepared pan. Spread cream cheese mixture over pumpkin batter. Sprinkle with ½ cup chocolate chips.
Bake until edges begin to pull away from sides of pan and cheesecake is set, about 45 minutes. Cool completely in pan.
Lift bars from pan (using foil as an aid). Peel off foil, and use a serrated knife to cut into 16 squares.