Preheat oven to 350 degrees F (175 degrees C). Line 12 muffin cups with paper liners.
Mix almond meal and butter together in a bowl; spoon into the bottoms of the paper liners and press into a flat crust.
Beat cream cheese, eggs, sweetener, and vanilla extract together in a bowl with an electric mixer set to medium until smooth; spoon over the crust layer in the paper liners.
Bake in the preheated oven until the cream cheese mixture is nearly set in the middle, 15 to 17 minutes.
Let cupcakes cool at room temperature until cool enough to handle. Refrigerate 8 hours to overnight before serving.
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