Prep the pan: Heat oven to 325°F (165°C). Line the bottom of a 9-inch springform pan with parchment.
Lightly grease the sides.
Make the crust: In a bowl, combine almond flour, melted butter, sweetener, cinnamon, and salt until it resembles damp sand. Press evenly into the pan. Bake 8–10 minutes, just until set and lightly golden.
Cool while you make the filling.
Blend the dairy base: In a food processor, blend cottage cheese until completely smooth, 1–2 minutes. Add cream cheese and Greek yogurt; blend again until uniform and silky.
Add flavor and protein: Add sweetener, vanilla, lemon juice, salt, and protein powder. Pulse until smooth.
Taste and adjust sweetness if needed.
Incorporate eggs: Add eggs one at a time, pulsing briefly after each. Do not overmix—just until combined. Overmixing adds air and can cause cracks.
Fill and smooth: Pour the filling onto the crust.
Tap the pan gently on the counter a few times to release air bubbles. Run a spatula over the top to even it out.
Bake low and slow: Bake at 325°F for 35–45 minutes. The edges should be set and the center should have a gentle jiggle.
If it browns too quickly, tent loosely with foil.
Cool gradually: Turn off the oven, crack the door, and let the cheesecake sit inside for 30 minutes. Then cool on the counter for another 30 minutes.
Chill completely: Cover and refrigerate at least 4 hours, preferably overnight, to set the texture.
Toast the pecans: While it chills, toast pecans in a dry skillet over medium heat for 3–4 minutes until fragrant. Cool and chop.
Add toppings: Melt chocolate chips with coconut oil in short microwave bursts, stirring until smooth.
Drizzle chocolate and caramel over the chilled cheesecake. Sprinkle with toasted pecans and a pinch of flaky sea salt.
Slice cleanly: Run a knife around the edge before releasing the springform. Warm a sharp knife under hot water, wipe dry, and slice.
Clean the knife between cuts.