Preheat the oven to 325 degrees F and line the cups of a muffin tin ith cupcake liners. Set aside.
Whisk together the graham cracker crumbs, melted butter, sugar, cinnamon, and nutmeg in a medium mixing bowl until crumbs are evenly moistened.
Add around 1 1/2 tablespoons of graham cracker crumbs to each of the muffin cups. Press down on the crumbs with a spoon or use a glass to form the crusts. Set aside.
To make the streusel: Whisk together the flour, sugar, cinnamon, nutmeg, and salt in a mixing bowl. Add the cold butter and work it into the dry ingredients with your fingertips or a fork until it comes together to form little crumbles and the butter chunks are no longer visible. Refrigerate while you prepare the apples and filling.
To make the apple layer: Combine the chopped apples with brown sugar in a bowl and put aside to macerate.
To make the cheesecake filling: Beat together the cream cheese, powdered sugar, vanilla, and sour cream in a medium medium bowl with a whisk or hand mixer until smooth. Mix in the egg until incorporated. Set aside.
To assemble the cheesecakes: Add 1 1/2 tablespoons of cheesecake filling to each muffin tin cup. Divide the apples evenly over the cheesecake layer (be sure to get some of the liquid from the apple bowl on each one too!) and then top with a heaping tablespoon of the streusel.
Bake the cheesecakes for 23 to 25 minutes until the filling is almost set and the topping is turning golden brown.
Let cheesecakes cool down at room temperature before transferring them to the fridge to chill for at least 1 hour. Use a spoon to drizzle some caramel sauce over the cheesecakes and enjoy!
Notes
These cheesecakes will keep for up to 4 days in the fridge in an airtight container.