Preheat oven to 350 degrees F. Line a muffin tin with cupcake liners and set aside.
Mix the sugar, eggs, pumpkin puree, and vegetable oil until well combined.
Add the all-purpose flour, cinnamon, nutmeg, salt, baking powder, and baking soda and mix but do not overmix.
Pour the batter into the cupcake liners, filling it 3/4s of the way up.
To make the cream cheese filling, simply mix the softened cream cheese, 1 tsp flour, and 2 tbsp sugar until well combined. Mix well.
Add about 1 tbsp of the cheesecake filling to the center of each cupcake liner. Do not swirl.
Bake for 20 minutes.