Prep your pan and oven: Line a 12-cup muffin pan with paper liners or use silicone molds. Preheat to 325°F (165°C). This slightly lower temperature helps prevent cracks and rubbery texture.
Make the optional crust: In a bowl, mix almond flour, melted butter, sweetener, and a pinch of salt.
Divide evenly among liners, about 1 tablespoon each. Press firmly. Par-bake for 6–7 minutes until lightly set, then cool while you make the filling.
Soften the cream cheese: Make sure it’s truly soft.
If it’s still cool, microwave in short 10-second bursts. Soft cream cheese blends smoother, which means fewer lumps.
Beat the base: In a mixing bowl, beat cream cheese with sweetener until fluffy and smooth, 1–2 minutes. Scrape down the bowl so no streaks remain.
Add the egg and vanilla: Beat in the egg and vanilla until just combined.
Don’t overmix here—too much air can cause sinking.
Fold in yogurt and protein: Add Greek yogurt and protein powder. Mix on low or fold with a spatula until no dry pockets remain. The batter should be thick but scoopable.
If it’s too thick, stir in 1–2 tablespoons milk or almond milk to loosen.
Stir in the chips: Fold in mini chocolate chips. Reserve a few for the tops if you want a bakery-style look.
Fill the cups: Divide batter among the liners, about 2 heaping tablespoons each, nearly to the top. Smooth the surfaces with the back of a spoon.
Sprinkle reserved chips.
Bake: Place the pan on the middle rack and bake for 14–18 minutes. They’re done when edges are set and the centers have a slight jiggle. Don’t wait for them to be fully firm in the oven.
Cool gradually: Turn off the oven, crack the door, and let the cups rest for 5 minutes.
Move the pan to a rack and cool to room temp, about 30 minutes. This gentle cooling helps prevent cracks.
Chill: Refrigerate for at least 2 hours, uncovered for the first 30 minutes to prevent condensation, then covered. They set fully as they chill.
Serve: Enjoy straight from the fridge, or let them sit 5–10 minutes to soften.
Add a few extra chips or a dollop of yogurt if you like.