In the bowl of an electric mixer, mix together on low speed: the cream cheese, pure cane sugar, and flour until combined. Be sure to scrape the sides and bottom of the bowl if needed.
In the bowl of an electric mixer, mix together on low speed: the cream cheese, brown sugar, and flour until combined. Be sure to scrape the sides and bottom of the bowl if needed.
Next, add the vanilla extract and the first egg and beat slowly until mostly combined. Then add the remaining egg and mix until well combined, still mixing everything on low speed. Now, add the sour cream, cinnamon, nutmeg, and salt and continue mixing.
Change mixer attachment to a whisk and beat on medium-high speed for 5 minutes or so until completely smooth and lump-free.
Add a small amount of filling to each cupcake liner (about 2 Tbsps), repeating until all batter is used.
Bake the cheesecakes for 20-25 minutes, then turn off the oven and allow them to sit in the oven for another 5 minutes with the oven door halfway open to avoid cheesecakes from deflating. NOTE: When baking, I always prepare a medium pot with water and add it to the oven as well, to keep cheesecake temperature even and to add moisture.
Remove cheesecakes from the oven and allow them to continue to cool for another 15-20 minutes or until at room temperature coolness, before putting them in the refrigerator for at least an hour.
In the meantime, make your 'pecan pie' topping.