Preheat oven to 325°F (163°C). Line a muffin tin with cupcake liners.
Make the crust: In a bowl, mix graham cracker crumbs, brown sugar, cinnamon, and melted butter. Press about 1-2 tablespoons into each liner and compact with the bottom of a measuring cup.
Prepare cheesecake filling: Beat softened cream cheese and sugar until smooth. Add eggs, vanilla, and sour cream. Beat until just combined.
Make apple topping: In a bowl, combine diced apples with brown sugar, cinnamon, nutmeg, cornstarch, and lemon juice. Let sit for 10 minutes.
Make crumble topping: Mix flour, oats, brown sugar, and cinnamon. Cut in cold butter until crumbly with pea-sized bits.
Assemble cheesecakes: Spoon cheesecake filling over crusts until ¾ full. Add a spoonful of apple topping, then sprinkle crumble on top.
Bake for 22–25 minutes or until edges are set and centers jiggle slightly. For best results, place a pan of hot water on the lower oven rack to prevent cracking.
Cool completely in the pan. Refrigerate at least 2 hours before serving.
Optional: Garnish with whipped cream and a sprinkle of cinnamon before serving.