Preheat the oven to 325-degrees. Line the cups of the muffin tins with paper liners and place a vanilla wafer in the bottom of each.
In a large mixing bowl beat the cream cheese until light and very smooth, about 3 minutes. Scrape the sides and bottom of the bowl, making sure the cream cheese is free of lumps. Whisk the sugar and flour together and add to the cream cheese, mixing well on low speed.
Add the eggs one at a time, blending in on low speed.
Stir in the vanilla extract and the lemon paste along with the lemon zest, lemon juice, and heavy cream.
Divide the batter between each of the muffin cups, about ¾ full and bake for 25 minutes until the cheesecakes are set.
While the cheesecakes bake, stir the yogurt together with the sugar, vanilla, lemon paste, lemon zest, and lemon juice.
When the cheesecakes are set remove from the oven. The cheesecakes will be puffed coming out of the oven but sink slightly in the center when removed. Spoon a dollop of the yogurt topping on the tops of each cupcake. Return to the oven and bake for an additional 5 minutes.
Remove the cheesecakes from oven and when cool enough to handle, about 5 minutes, gently remove from the tins and cool completely on a wire rack.
Once they’re completely cool, place the cupcakes in a sealed container and refrigerate until ready to serve.
These can be made a day or two in advance and serve chilled or served warm straight from the oven, with a sprinkling of lemon zest.