Preheat oven to 350°F and line an 8x8 or 9x9 baking dish with parchment paper.
Mix graham cracker crumbs, sugar, and melted butter until combined, then press into the bottom of the dish to form a crust. Bake for 8 minutes, then let cool slightly.
In a bowl, beat cream cheese and sugar until smooth. Add eggs one at a time, then mix in vanilla. Pour over the crust.
Toss the diced apples with sugar, cinnamon, and nutmeg. Sprinkle evenly over the cheesecake layer.
Bake for 35–40 minutes, or until the center is set and doesn’t jiggle. Cool completely, then refrigerate for at least 3 hours.
Drizzle with caramel sauce just before serving and slice into bars.