In a medium bowl, stir together the softened cream cheese, sugar, vanilla extract, and pumpkin pie spice until smooth and creamy.
Portion the filling into rounded 1 tablespoon balls onto a parchment-lined plate or baking sheet. Freeze for about 1 hour, or until completely solid. Do not flatten the balls.
Make the Pumpkin Cookie Dough
In a medium bowl, whisk together the whole wheat flour, pumpkin pie spice, baking powder, baking soda, and salt.
In a large bowl, cream the softened butter and sugar until combined and creamy. Beat in the egg, pumpkin purée, and vanilla extract until incorporated.
Gradually add the dry ingredients to the wet ingredients, mixing just until combined. Cover and refrigerate for at least 1 hour, or until the dough is firm enough to handle.
Assemble the Cookies
Preheat the oven to 350°F (175°C) and line a baking sheet with parchment paper. In a shallow bowl, mix the sugar, cinnamon, and ginger for the coating.
Scoop approximately 3 tablespoons of chilled cookie dough and flatten it in your palm. Place one frozen cheesecake ball in the centre, then carefully wrap the dough around it, pinching the edges to seal completely.
Gently roll the stuffed dough into a ball, then roll it in the cinnamon sugar mixture until coated. Place on the prepared baking sheet, about 3 inches apart. Do not flatten the assembled cookies. Repeat with the remaining dough and filling.
Bake and Cool
Bake for approximately 15 to 20 minutes, or until the edges are set and lightly golden and the tops no longer look wet. The centres should still be slightly soft.
Let the cookies rest on the baking sheet for about 10 minutes before transferring them to a wire rack to cool completely. This helps the cheesecake filling set.
Notes
Use plain pumpkin purée, not pumpkin pie filling. The added sugar and spices in pie filling can affect the cookies.Freeze the cheesecake filling until solid. Keep the portions rounded, not flattened, for a thick, creamy centre.Work with cold ingredients. If the filling starts softening while you're assembling the cookies, pop it back in the freezer for a few minutes.Don't flatten the cookies! Keep the stuffed dough balls rounded before baking so the cheesecake centre stays nice and pronounced.Don't overbake. The edges should be set and lightly golden, but the centres will still be soft. They'll firm up as they cool.Refrigerate leftovers in an airtight container for up to 5 days, or freeze baked cookies for up to 2 months.