Lemon Cheesecake Cupcakes

Makes 12

This recipe makes a classic New York cheesecake baked in a muffin tin.

Topped with whipped cream frosting or fresh summer berries, our Lemon Cheesecake Cupcakes will be your new favorite gluten-free dessert. 


  • Cupcakes:
  • 12 gluten-free vanilla wafer cookies
  • 16 ounces cream cheese, at room temperature
  • ½ cup sour cream
  • ½ cup granulated sugar
  • Zest of one lemon
  • 1 tablespoon freshly squeezed lemon juice
  • 2 large eggs, room temperature
  • ----------
  • Whipped cream topping:
  • 1 cup heavy cream (whipping cream)
  • ¼ cup sifted powdered sugar
  • 1 teaspoon vanilla extract


Preheat oven to 325° F. Line a 12-cup muffin pan with paper liners. Place a vanilla wafer in the bottom of each muffin cup. Set aside.

Combine cream cheese, sour cream, sugar, lemon zest and juice in a large bowl. Mix on low speed with a handheld mixer. Scrape the sides and bottom of the mixer with a rubber spatula. Mix again. Add the eggs. Mix until combined.

Spoon batter into prepared muffin cups.

Bake until set, about 20 minutes. Turn off oven. Allow cheesecakes to cool in the oven for 30 minutes. Cheesecakes puff during baking and often sink as they cool.

Remove cheesecakes from pan. Allow to cool completely. Prepare topping. Whip together heavy cream, powdered sugar and vanilla extract until smooth. Dollop topping on cooled cheesecakes.

Store leftovers wrapped in the refrigerator for up to four days.

Preparation time: 10 minutes. Cooking time: 20 minutes.