Making The Gluten-Free Crust: Preheat your oven to 350 degrees F. In a bowl, mix together the graham cracker crumbs, melted butter, sugar, and salt. Press the cheesecake crust mixture into the bottom of a 9-inch springform pan using your hands or a glass and bake for 9-12 minutes.
Making The Cheesecake Filling - In a large bowl with a hand held mixer or in the bowl of a stand mixer with the paddle attachment, beat the cream cheese and sugar together until smooth. Add the eggs, one at a time, fully incorporating each before adding the next. Stir in the Greek yogurt, vanilla extract, and salt.
Pour the filling over the crust in the springform pan. Smooth the top with a spatula and tap the pan on the counter numerous times to release any air bubbles.
Reduce the oven temperature to 325 degrees F. Place a baking dish into the oven underneath the cheesecake and add hot water to create a water bath. Approximately 1-2 inches of water.
Bake for 75 minutes, or until the center is just set and the edges are lightly golden. Turn off the oven, open the door slightly and keep it cracked open with a wooden spoon. Let the cheesecake cool inside for 1 hour to prevent cracks.
Remove the cheesecake from the water bath and allow it to reach room temperature. Cover and let chill in the fridge for minimum 4 hours to overnight.
Making The Apple Pecan Topping - Once creamy cheesecake filling has set, make the pecan apple topping. In a medium pan over medium heat, melt the butter and brown sugar together until combined and bubbling slightly. Add the apples, cinnamon, and nutmeg, then cook for 7-9 minutes, stirring occasionally, until the apples are tender.
Stir in the pecans until they’re well coated and evenly mixed. Pile the cinnamon-spiced apple pecan topping right on top of your creamy cheesecake layer.
When you’re ready to serve, run a knife around the edge of the pan, then release and remove the springform. Slice, serve, and watch as everyone falls in love with this gluten-free delight!