Prep the pan. Heat your 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, mix almond flour, cocoa, sweetener, and salt. Stir in melted butter and vanilla until the mixture resembles damp sand and holds when pressed. Press firmly into the bottom of the pan in an even layer.
Par-bake the crust. Bake for 8–10 minutes until slightly darkened and set.
Cool for at least 10 minutes while you make the filling.
Beat the cream cheese. In a large bowl, beat cream cheese on medium speed until completely smooth and no lumps remain. This step prevents a grainy filling.
Add yogurt and sweetener. Mix in Greek yogurt and granulated sweetener until silky. Scrape the bowl so everything is combined.
Blend in dry ingredients. Sift in cocoa powder and protein powder to avoid clumps.
Add salt. Mix on low until just combined. If the batter feels too thick, add milk a tablespoon at a time until it’s luxuriously smooth but not runny.
Flavor it. Beat in peppermint and vanilla extract.
Taste the batter and adjust mint or sweetness. If using food coloring, add a drop or two for a pale mint color.
Add the eggs. Beat in eggs one at a time on low speed, just until incorporated. Overmixing can introduce air and cause cracks.
Fill and smooth. Pour the filling over the cooled crust.
Tap the pan gently on the counter to release air bubbles. Smooth the top with a spatula.
Bake low and slow. Bake at 325°F (165°C) for 35–45 minutes. The edges should be set, and the center should still wobble slightly like gelatin.
Do not overbake.
Cool gradually. Turn off the oven, crack the door, and let the cheesecake rest inside for 30 minutes. Then transfer to a rack to cool to room temperature.
Chill to set. Cover and refrigerate at least 6 hours, preferably overnight. This step firms up the texture and deepens the flavor.
Add the chocolate top. Melt chocolate with coconut oil in short bursts in the microwave or over a double boiler.
Let it cool slightly, then drizzle or spread thinly over the cold cheesecake. It will set into a light shell.
Slice and serve. Run a knife around the pan edge, release the springform, and slice with a hot, clean knife for tidy pieces. Garnish with mint leaves if you like.