Prep the pan. Line a 12-cup muffin tin with paper liners. Preheat your oven to 325°F (165°C).
This slightly lower heat helps the cups bake gently and stay creamy.
Make the crust. In a bowl, combine chocolate crumbs, cocoa, sweetener, melted coconut oil or butter, and a pinch of salt. Stir until the mixture looks like damp sand and clumps when pressed.
Press and par-bake. Divide the crust mixture evenly among the liners (about 1 heaping tablespoon each). Press firmly with the back of a spoon.
Bake 5–6 minutes to set, then cool while you make the filling.
Beat the cream cheese. In a large bowl, beat the softened cream cheese until very smooth, about 1 minute. Scrape the bowl well. Smooth cream cheese prevents lumps later.
Add the yogurt, sweetener, and vanilla. Mix in Greek yogurt, sweetener, vanilla, and salt until silky.
Taste and adjust sweetness now—protein and cocoa can mute sweetness slightly.
Blend in cocoa and protein powder. Add cocoa and chocolate protein powder. Mix on low just until combined. If the batter seems too thick, add 1–2 tablespoons milk to loosen.
Avoid overmixing to keep it creamy.
Beat in eggs. Add eggs one at a time, mixing on low until just incorporated. Don’t whip in too much air, or your cheesecakes can puff and crack.
Fill the cups. Spoon the filling over crusts, filling each liner almost to the top. Smooth the surface with the back of a spoon.
Bake gently. Bake at 325°F (165°C) for 14–18 minutes.
They’re done when edges are set but centers still wobble slightly. A little jiggle is perfect.
Cool and chill. Let the cups cool in the pan for 30 minutes, then transfer to the fridge. Chill at least 3 hours, preferably overnight, to fully set and develop flavor.
Top and serve. Add a dollop of whipped topping, berries, or a sprinkle of dark chocolate.
Enjoy straight from the fridge for the best texture.