Preheat oven to 325°F (163°C). Line a muffin tin with 12 cupcake liners.
In a bowl, combine graham cracker crumbs, sugar, and melted butter. Press about 1 tablespoon into each liner to form the crust. Bake for 5 minutes and let cool.
In a large bowl, beat cream cheese until smooth. Add sugar and vanilla, mix until combined. Add eggs one at a time, mixing after each.
Divide the cheesecake filling evenly over the crusts in the liners.
In a small bowl, mix chopped apples, brown sugar, cinnamon, nutmeg, and lemon juice. Spoon the mixture over the cheesecake layer in each cup.
To make the crisp topping, mix oats, flour, brown sugar, and cold butter until crumbly. Sprinkle evenly over the apple layer.
Bake for 25–30 minutes, until the centers are set. Let cool completely, then refrigerate for at least 2 hours before serving.
