Prep the pan and oven: Line a 12-cup muffin pan with paper liners. Preheat oven to 325°F (165°C). This lower temp helps prevent cracks.
Make the crust: Stir 1 cup graham cracker crumbs with 2 tablespoons sugar, a pinch of salt, and 4 tablespoons melted butter until it looks like wet sand.
Press about 1 to 1.5 tablespoons into each liner. Use a flat-bottom glass to pack it firmly. Bake for 5 minutes, then set aside.
Cook the apples: Peel and dice 2 medium apples into small cubes.
In a saucepan, melt 1 tablespoon butter, then add apples, 2 tablespoons brown sugar, 1/2 teaspoon cinnamon, a pinch of nutmeg, and 1 teaspoon lemon juice. Cook 4–6 minutes until just tender. Stir in 1 teaspoon cornstarch to thicken.
Remove from heat and let cool slightly.
Mix the crisp topping: Combine 1/2 cup rolled oats, 1/3 cup flour, 1/3 cup brown sugar, 1/2 teaspoon cinnamon, a pinch of salt, and 3 tablespoons melted butter. Stir until clumpy. Set aside.
Make the cheesecake batter: Beat 16 ounces softened cream cheese with 1/2 cup granulated sugar until smooth, about 1–2 minutes.
Mix in 1/3 cup sour cream and 1 teaspoon vanilla. Beat in 2 room-temperature eggs, one at a time, on low speed just until incorporated. Do not overmix.
Fill the cups: Divide cheesecake batter evenly among the crusts, filling each about 3/4 full. Gently tap the pan to release air bubbles.
Add apples and crisp: Spoon a heaping teaspoon of the cooked apples over each mini cheesecake.
Crumble a tablespoon or so of the oat topping over the apples, covering the surface but not overfilling.
Bake: Bake at 325°F for 18–22 minutes, until edges are set and centers still jiggle slightly. The crisp topping should look golden.
Cool properly: Turn off the oven and prop the door open for 5 minutes. Move the pan to a rack and cool to room temperature. Do not rush this step or you’ll risk sunken centers.
Chill: Refrigerate at least 2 hours (overnight is best) to fully set.
Remove liners before serving if you like.
Finish and serve: Drizzle with caramel and a pinch of flaky salt, or add a small dollop of whipped cream. Serve chilled or slightly cool.