Prep the pan. Line the bottom of a 9-inch springform pan with parchment.
Lightly grease the sides. Heat oven to 325°F (165°C).
Make the crust. In a bowl, mix almond flour, shredded coconut, cocoa, sweetener, and salt. Stir in melted butter and vanilla until it looks like damp sand.
Press and par-bake. Firmly press the crust into the bottom of the pan.
Use a flat-bottom glass to even it out. Bake for 10 minutes. Set aside to cool while you make the filling.
Toast the coconut for topping. Spread coconut on a small sheet pan and toast at 325°F for 4–6 minutes until lightly golden.
Watch closely. Set aside to cool.
Beat the cream cheese. In a large mixing bowl, beat cream cheese on medium speed until completely smooth, about 1–2 minutes. Scrape the bowl.
Add yogurt and sweetener. Mix in Greek yogurt and sweetener until smooth.
Scrape down the sides again.
Blend dry ingredients. In a small bowl, whisk cocoa powder, whey isolate, and salt. Sift into the batter to avoid lumps. Mix on low until combined.
Flavor and eggs. Add coconut and vanilla extracts.
Beat in eggs one at a time on low speed just until incorporated. Do not overmix to avoid adding too much air.
Fill the pan. Pour the filling over the crust. Tap the pan on the counter a few times to release air bubbles.
Bake low and slow. Bake at 300°F (150°C) for 55–70 minutes. The edges should be set and the center slightly wobbly like Jell-O.
If your oven runs hot, tent lightly with foil at the 45-minute mark.
Cool gradually. Turn off the oven, crack the door, and let the cheesecake rest inside for 45 minutes. Then remove and cool to room temperature.
Chill. Cover and refrigerate at least 6 hours, preferably overnight, to set and develop flavor.
Add the topping. Melt chocolate chips gently (microwave in 15-second bursts or use a double boiler). Stir in heavy cream until glossy and pourable.
Spread a thin layer over the chilled cheesecake and sprinkle with toasted coconut.
Slice cleanly. Warm a sharp knife under hot water, wipe dry, and cut. Repeat between slices for neat edges.