Prep the pan and oven: Heat oven to 325°F (163°C). Grease a 9-inch pie plate or springform pan and line the bottom with parchment if using a springform.
Make the crust: In a bowl, mix almond flour, coconut flour, sweetener, cinnamon, and salt.
Stir in melted butter and vanilla until the mixture resembles damp sand.
Press and pre-bake: Press the crust evenly into the pan and up the sides. Prick the bottom with a fork. Bake for 10–12 minutes until lightly set and just golden at the edges.
Cool for 10 minutes.
Beat the cheesecake layer: With a hand mixer, beat 8 oz cream cheese until smooth. Add sour cream, sweetener, vanilla, and salt; beat until fluffy. Beat in 1 egg just until combined.
Do not overmix.
Spread the cheesecake base: Pour into the cooled crust and smooth into an even layer. Chill in the freezer for 10 minutes to slightly firm.
Mix the pumpkin layer: Beat remaining 8 oz cream cheese until smooth. Add pumpkin puree, sweetener, vanilla, pumpkin pie spice, cinnamon, and salt.
Mix well. Beat in the 2 eggs one at a time just until smooth.
Layer gently: Spoon the pumpkin mixture over the cheesecake base. Use an offset spatula to smooth the top without disturbing the layer below.
Bake low and slow: Bake at 325°F for 40–50 minutes.
The edges should be set and the center should jiggle like soft Jell-O when you gently nudge the pan.
Cool gradually: Turn off the oven, crack the door, and let the pie sit for 15 minutes. Transfer to a rack and cool to room temperature.
Chill to set: Cover and refrigerate at least 4 hours, preferably overnight, for clean slices and the best flavor.
Serve: Top with whipped cream and a sprinkle of cinnamon or chopped pecans. Slice with a warm, clean knife for neat edges.