Prep the pan and oven: Heat oven to 325°F (163°C). Line the bottom of a 9-inch springform pan with parchment.
Lightly grease the sides. Wrap the outside with foil to catch any drips.
Make the crust: In a bowl, mix chopped pecans, almond flour, brown sugar, salt, and melted butter. It should resemble damp sand and hold when pressed.
Press evenly into the bottom of the pan. Bake 8–10 minutes until fragrant. Cool while you make the filling.
Beat the cream cheese: In a large bowl, beat softened cream cheese until smooth and lump-free, about 1–2 minutes.
Scrape the bowl often to avoid clumps.
Add sweetener and yogurt: Mix in sugar and Greek yogurt until silky. Avoid overbeating, which can add excess air.
Blend in dry ingredients: Add protein powder, cornstarch, salt, and vanilla. Mix on low until just combined.
The batter will be thick but pourable.
Add eggs last: Beat in eggs one at a time on low, stopping when just incorporated. Overmixing can cause cracks.
Fill and bake: Pour the filling over the crust and smooth the top. Bake at 325°F for 40–50 minutes.
The edges should look set and the center should wobble slightly like gelatin.
Cool gently: Turn off the oven, crack the door, and let the cheesecake sit for 30 minutes. Then move to a rack and cool to room temperature. This slow cool helps prevent cracks.
Chill completely: Cover and refrigerate for at least 6 hours, preferably overnight.
Cold cheesecake slices cleanly and tastes better.
Make the pecan pie topping: In a small saucepan, heat butter, maple syrup, and brown sugar over medium heat until bubbling. Stir in vanilla and salt. Add the cornstarch slurry and cook 30–60 seconds until glossy and slightly thickened.
Stir in pecan halves to coat.
Top the cheesecake: Let the topping cool for 5–10 minutes until thick but still spreadable. Spoon over the chilled cheesecake, pushing nuts to the edges. Chill 20–30 minutes to set.
Slice and serve: Run a warm knife around the edge, release the springform, and slice with a hot, clean knife for neat edges.