Preheat the oven to 350 degrees F (175 degrees C). Line 12 muffin cups with paper liners.

Mix together almond meal and melted butter in a small bowl until well combined; spoon into the bottoms of the paper liners and press into a flat crust.

Beat together cream cheese, sweetener, eggs, and vanilla in a large bowl with an electric mixer on medium speed until smooth. Spoon evenly over crust layer in the paper liners.

Bake in the preheated oven until cream cheese mixture is nearly set in the centers, 15 to 17 minutes. Let cupcakes cool at room temperature until cool enough to handle. Refrigerate before serving, 8 hours to overnight.