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Cheesecake Cupcakes are a bite-sized cheesecake treat. Top with cherry pie filling, or any other topping you like!

These sweet treats are the perfect crossroad between cheesecake and cupcakes. They’re creamy, delicious, and bite sizes, just like out Mini Peanut Butter Cheesecakes.

Cherry cheesecake cupcakes sitting on a wire rack


Cheesecake and Cupcakes in One!

I LOVE baking! The creativity and fun that comes with baking are just so exciting to me! Combine recipes and ingredients to make new unique creations—and that’s exactly what this recipe is.

A cheesecake cupcake is the perfect combination of two of the best desserts: cheesecake and cupcakes! I will say it is more cream cheese-y than cakey, so if you enjoy cheesecake, you will love these little bites.

You could top the cupcakes with any topping you like, but the cherry pie filling complimented the base just perfectly! It made the yummiest combination of sweet and tart.

Cheesecake cupcakes in a muffin tin ready to be baked.

Just 6 Ingredients!

Believe it or not, you can whip up these simple little treats with just 6 ingredients and a hand mixer.

BEAT. In a large bowl, beat cream cheese, 1 cup sugar, and 1 tsp vanilla until smooth. Add eggs, one at a time, beating after each addition. Spoon into foil-lined muffin cups.

BAKE. Bake for 25-30 minutes at 300°F. A toothpick inserted in the center should come out clean. Cool for at least 5 minutes.

2ND LAYER. In a small bowl, combine sour cream and remaining sugar, and vanilla until smooth. Spoon on top of cupcakes.

BAKE. Bake for an additional 6-8 minutes, until set. Cool for 10 minutes before moving to wire racks to cool completely.

TOP. Top with cherry pie filling (or a different pie filling of choice) and serve.

Graham Cracker Crust

Try these Mini Cherry Cheesecakes with a Graham Cracker Crust.

You’ll need 1⅛ cups of graham cracker crumbs, 2½  tablespoons of sugar, and ⅓ cup of melted butter.

  1. Preheat the oven to 350°F.
  2. Place cupcake liners into the cupcake pan. 
  3. In a medium bowl combine crust ingredients. Divide it evenly between the 18 cupcake liners. Press the crumbs firmly into the liners.
  4. Bake for 5 minutes. Cool completely before adding the cream cheese mixture. Complete the recipe as instructed.
Topping cheesecake cupcakes with cherry filling topping.

Recipe Tips

Toppings. A really fun way to serve these cream cheese cupcakes is to set out a variety of toppings and let your guests choose which one to use.

Foil liners. Use regular-size cupcake foils or reusable silicone cupcake liners. I do not suggest using paper liners as the bottom of the cheesecake is more likely to burn. The cheesecake also tends to stick more to the paper liner when it is peeled off than the foil ones.

Room temperature. Using room-temperature eggs, sour cream, and cream cheese will help them all incorporate better with one another.

Mini cherry cheesecakes in cupcake liners on a wire rack.

Storing Tips

STORE. Cover and store leftover cupcakes in an airtight container in the fridge for 5-7 days.

FREEZE. You can freeze leftover cupcakes with or without topping. For plain cupcakes, wrap each cheesecake with plastic wrap and store them all in a freezer-safe container.

If the cupcakes have pie filling on top, flash freeze first.

  • Place all the cupcakes on a baking sheet and freeze for 2-3 hours or until the top has hardened.
  • Wrap individually with plastic wrap and then place in an airtight freezer-safe container.

Frozen cheesecakes can last for about 6 months in the freezer. Before eating, remove the plastic wrap and thaw them in the fridge.

Close up of mini cherry cheesecake cupcakes topped with cherry pie filling.

Recipe FAQ

How do you keep cheesecake cupcakes from sinking?

Be sure to use room temperature ingredients. Cold ingredients require longer mixing time, which adds air to the batter. Air causes it to rise too much in the oven and sink in the middle when it cools.

Do I need to use foil cupcake liners?

I recommend using cupcake foils or reusable silicone cupcake liners. When using paper liners, the bottom of the cheesecake is more likely to burn. The cheesecake also tends to stick more to the paper liner when it’s peeled off.

What can I use besides cherry pie filling?

Use any flavor of pie filling such as blueberry, raspberry, or strawberry pie filling. You could also use Chocolate Sauce, Caramel Sauce, or Nutella and drizzle it over the top.

For more great cheesecake recipes, try:

4.94 from 32 votes

Cheesecake Cupcakes Recipe

By: Lil’ Luna
Cherry Cheesecake Cupcakes are a bite-sized cheesecake treat. They're sweet, tart, and ultra simple to make!
Servings: 18
Prep: 10 minutes
Cook: 30 minutes
Total: 40 minutes

Ingredients 

  • 3 (8-ounce) packages cream cheese softened
  • cups sugar divided
  • teaspoons vanilla extract divided
  • 5 eggs
  • 1 cup sour cream
  • cups cherry pie filling

Instructions 

  • Preheat oven to 300℉.
  • In a large bowl, beat cream cheese, 1 cup sugar, and 1 teaspoon vanilla until smooth. Add eggs, one at a time, beating after each addition. Spoon into foil-lined muffin cups
  • Bake for 25-30 minutes. Toothpick inserted in the center should come out clean. Cool for at least 5 minutes.
  • In a small bowl, combine sour cream and remaining sugar and vanilla until smooth. Spoon on top of cupcakes. Bake for an additional 6-8 minutes, until set. Cool for 10 minutes before moving to wire racks to cool.
  • Top with pie filling. ENJOY! Store in the refrigerator.

Video

Nutrition

Calories: 293kcal, Carbohydrates: 32g, Protein: 4g, Fat: 16g, Saturated Fat: 9g, Cholesterol: 93mg, Sodium: 158mg, Potassium: 139mg, Sugar: 18g, Vitamin A: 755IU, Vitamin C: 1.9mg, Calcium: 63mg, Iron: 0.5mg

Nutrition information is automatically calculated, so should only be used as an approximation.

Additional Info

Course: Dessert
Cuisine: American
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About Kristyn

My name is Kristyn and I’m the mom of SIX stinkin’ cute kids and the wife to my smokin’ hot hubby, Lo. My mom’s maiden name is Luna, and I’m one of the many crafty “Lil’ Lunas” in the fam. On this site I like to share all things creative - from recipes to home decor to gifts and home decor ideas. Welcome!

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Recipe Rating




32 Comments

  1. 5 stars
    I was so excited to find this awesome recipe, as I’ve used this same one for years, but lost it in a move. I’ve never made these in regular sized cups, only the mini (I also add a tiny bit of almond extract to mine, freeze them to have on hand for munchies.), so the larger size will be great to take for football tailgating and watch parties and other events!
    I really enjoy your website! Thank you for sharing your recipes!