Line a 12-cup muffin tin with paper liners (or silicone baking cups for easy removal). Preheat the oven to 350°F (175°C). This smaller, individual format helps the cheesecakes bake evenly and chill quickly later on.
In a medium mixing bowl, combine the almond meal and melted butter. Use a fork to mix until the texture resembles slightly damp sand and the crumbs begin to clump together.
Evenly divide the crust mixture among the 12 muffin liners—about 1 to 1½ tablespoons per cup. Use the back of a spoon or the bottom of a small glass to firmly press the crust down into a compact, even layer. This helps it hold together once baked.
In a large bowl, whisk together the softened cream cheese, plain yogurt, vanilla protein powder, maple syrup, and vanilla extract until smooth and creamy. Scrape down the sides of the bowl as needed to make sure no lumps remain.
Tip: For the silkiest texture, make sure the cream cheese is fully softened before mixing—cold cream cheese can cause a grainy filling.
Use a muffin scoop or spoon to evenly divide the cheesecake filling between the liners, filling each about ¾ full. Smooth the tops gently with the back of a spoon or an offset spatula so they bake evenly.
Bake for 10 minutes, or until the edges are just set but the centers still have a slight jiggle. Avoid overbaking—mini cheesecakes will continue to firm up as they cool.
Remove the pan from the oven and let the cheesecakes cool in the pan for 15–20 minutes. Then transfer them to a wire rack to cool completely. Once cooled, place them in the refrigerator for at least 2 hours (or overnight) to set and develop flavor.
Store the cheesecakes in an airtight container in the refrigerator for up to 5 days. For longer storage, freeze them individually wrapped and thaw overnight in the fridge before serving.