Line a standard cupcake pan with 9 paper liners. Preheat your oven to 325°F (163°C) and set aside to ensure it's ready once you're finished assembling the cheesecake cupcakes.
In a mixing bowl, combine the graham cracker crumbs with 1 1/2 tablespoons of granulated sugar and 1/2 teaspoon of ground cinnamon. Stir together using a fork. Pour in 3 tablespoons of melted unsalted butter and mix thoroughly until the crumbs are evenly moistened. Press about 2 tablespoons of the mixture firmly into the bottom of each prepared cupcake liner, making sure the crusts are compact. Place the pan in the refrigerator to chill while you continue.
In a bowl, stir together 1/3 cup all-purpose flour, 1/3 cup packed light brown sugar, 1/3 cup quick oats, 3/4 teaspoon cinnamon, and 1/8 teaspoon ground nutmeg. Add 2 1/2 tablespoons melted unsalted butter, mixing until the mixture forms coarse crumbs. Place the crumble in the refrigerator until you’re ready to use. I love making extra crumble—it’s delicious sprinkled over yogurt, too!
In a medium mixing bowl, beat together the softened cream cheese, 6 tablespoons granulated sugar, 1 1/2 teaspoons vanilla extract, and 2 teaspoons all-purpose flour until smooth and creamy. Add in the egg and mix just until combined—try not to overmix. Spoon the cheesecake filling over the chilled crusts in each cupcake cup, filling them to about two-thirds full.
Peel and finely dice the apples. In a bowl, toss the diced apples with 2 teaspoons fresh lemon juice. Add 2 tablespoons light brown sugar, 1 1/2 teaspoons ground cinnamon, 1/4 teaspoon ground nutmeg, and 1 1/2 teaspoons cornstarch. Stir until the apples are evenly coated. Spoon the apple mixture over the cheesecake filling in each cupcake cup, filling nearly to the top. Gently press the apples down with your palm so they settle into the filling.
Generously sprinkle the prepared cinnamon oat crumble (from Step 3) over the apples in each cup, making sure each cupcake is well covered. Bake in the preheated oven for 28-30 minutes, or until the centers appear set and the topping is golden. I like to rotate the pan halfway through baking for even browning.
Allow the cheesecakes to cool for about 30 minutes in the pan. Then, remove them and chill in the refrigerator for several hours until fully set. Just before serving, drizzle with caramel sauce. For an extra treat, I sometimes gently warm the caramel before drizzling—the warmth adds an irresistible finishing touch.