Preheat oven to 325 degrees Fahrenheit and line a cupcake pan with cupcake liners and set aside.
In a food processor, grind up the graham crackers into fine crumbs and add the melted butter. Give everything a good mix so the butter evenly coats all of the graham crackers.
Press 2 tablespoons of the graham cracker mixture into the muffin cups wit the back of a spoon or measuring cup.
In a bowl of a stand mixer with the paddle attachment, mix the cream cheese until smooth and pour in the sugar and vanilla extract and continue mixing until combined and creamy.
Add in the eggs and into the cream cheese mixture until combined and then the sour cream and continue mixing until everything is mixed in well and smooth.
In another bowl, make the pumpkin puree mixture and combine the pumpkin puree, orange zest, pumpkin pie spice, brown sugar, orange zest and flour and whisk to combine.
Pour the cheesecake mixture into the muffin cups about ¾ way full to the top.
Add a few dollops of the pumpkin mixture into the cream cheese mixture and use a toothpick to swirl the pumpkin around the cheesecake batter.
Bake the cheesecakes for about 25-28 minutes until just set.
Once the cheesecake are done baking, place the muffin tin on a wire rack and let them cool completely before serving. Once cooled, place them in the refrigerator for at least 1 hour before serving.
Top cheesecakes with a dollop of whipped cream and freshly grated nutmeg.