Preheat oven to 325°F. Line 12 muffin cups with paper baking liners.
In the bowl of a stand mixer fitted with the paddle attachment or in a large bowl with an electric mixer, beat cream cheese for about two minutes.
In a medium bowl, combine sugar and lemon zest. Mix with your fingertips until sugar becomes moist and fragrant. Add lemon sugar to cream cheese and mix until light and fluffy. Add eggs, vanilla and lemon juice and mix until smooth.
Place a wafer (flat side down) in the bottom of each muffin cup. Spoon batter into each cup, filling each 2/3 full.
Bake in preheated oven for 22 to 24 minutes or until the centers are almost set. Cool in the pan on a wire rack. Note: The mini cheesecakes will deflate in the centers upon cooling. This is expected and leaves a nice spot to hold any toppings you choose to add.