Preheat the oven to 425 degrees F (220 degrees C).

Stir flour, butter, and 1/4 cup sugar together in a bowl until dough is well-blended. Pat dough into the bottom of a 9x13-inch baking dish.

Bake in the preheated oven until crust is lightly golden, 10 to 15 minutes. Cool. Reduce oven temperature to 350 degrees F (175 degrees C).

Beat cream cheese, 1/4 cup sugar, 1 egg, and vanilla together in a bowl with an electric mixer until smooth.

Whisk pumpkin puree, evaporated milk, 3/4 cup sugar, 2 eggs, cinnamon, salt, ginger, and cloves together in a bowl.

Spread cream cheese mixture evenly over cooled crust. Pour pumpkin mixture over cream cheese mixture.

Bake in the preheated oven until bars are set, about 60 minutes. Cool to room temperature, then refrigerate overnight.