Cherry cheesecake cupcakes are sweet vanilla cupcakes with a graham cracker bottom. They’re filled with fresh cherry filling and frosted with my favorite cream cheese buttercream. They’re like little cherry cheesecakes in cupcake form!

Cherry cheesecake cupcakes cut in half on a piece of parchment paper.

Today, we’re turning everyone’s favorite cherry cheesecake into cupcakes! They’re not as time-consuming or finicky as a whole cheesecake, and they still have all of the same flavors you love- buttery graham cracker crust, tangy cream cheese, and, of course, sweet red cherries!

These bakery-worthy cupcakes were inspired by my reader-favorite lemon raspberry cupcakes, except with cherries instead of raspberries. They’re perfect for summer and cherry season (like my chocolate cherry cake!) but can be enjoyed year-round, thanks to frozen cherries!

Tips for Bakery-Style Cupcakes

Use a kitchen scale. Baking with a scale is my #1 baking tip! If your cupcakes are dry and dense, it’s likely you’re not measuring the flour correctly.

Firmly press the crust. When making the graham cracker crust, firmly press the crumbs into the cupcake liners using the back of a spoon. This helps the crust hold together.

Fill the cupcake liners evenly. Use an ice cream or cookie scoop to distribute the batter. This ensures that the cupcakes bake evenly!

Use a cupcake corer. Use a cupcake corer or a small knife to remove the center of each cupcake for the cherry filling. This will create a neat hole for the filling.

Ingredient Notes and Substitutions

Ingredients needed to make cherry cupcakes in bowls with labels.

Frozen sweet red cherries: Like in my cherry pie bars, these cherries add a balanced, sweet flavor that complements the cupcakes without overpowering them. If you prefer a more tart filling, use sour cherries instead. You can also use cherry pie filling, although the flavor will be more intense and sweet.

Cake flour: This recipe uses cake flour for a super light and tender texture, and it should not be substituted! Using all-purpose flour will result in dry, tough cupcakes.

Sour cream: This ingredient adds moisture, richness, and tenderness, ensuring the cupcakes remain soft and moist for days! If needed, substitute with full-fat Greek yogurt.

Full-fat cream cheese: This is the best type of cream cheese for a thick yet fluffy frosting. Do not use low-fat or cream cheese that comes in a tub. Brick-style cream cheese is the only kind that will work!

Recipe Instructions

Step 1: Make the graham cracker crust. Combine the graham cracker crumbs, sugar, and melted butter. Spoon one tablespoon into each cupcake liner, pressing it into the bottoms. (Image 1 below)

Step 2: Combine the dry ingredients. In a stand mixing bowl, beat the butter into the dry ingredients until it has a crumbly consistency. (Image 2 below)

Step 3: Mix in the wet ingredients. Mix in the oil until pasty, then mix in the whisked milk, sour cream, egg, and vanilla, scraping down the bowl as needed, until the batter is smooth. (Image 3 below)

A process collage of the steps for making cherry cupcakes.

Step 4: Bake the cupcakes. Fill the cupcake liners 3/4 full with the batter. Don’t overfill! You will have enough batter to make roughly 13-14 cupcakes, so you may need to bake them in two rounds if you only have one cupcake pan. (Image 4 above)

Step 5: Make the cherry filling. Cook the cherries, mashing occasionally, until they have released their juices and are bubbling. Once thickened, transfer to a bowl and set aside to cool before using. (Image 5 below)

Step 6: Make the cream cheese frosting. Beat the frosting until light and fluffy. Do not beat it too fast, or the cream cheese will start to break down, be very thin, and will look wet. (Image 6 below)

A process collage of the steps for frosting and decorating the cherry cupcakes.

Step 7: Core and fill the centers. Use an apple corer to cut out the center of each cupcake (I eat them as snacks 😉). Then, use a piping bag or spoon to fill the centers with the cherry filling. Pipe a border of buttercream around the cherry-filled center. (Image 7 above)

Step 8: ​Frost and decorate the cupcakes. Roll the edges of the buttercream in the remaining graham cracker crumbs, then top with more cherry filling. Garnish with fresh cherries, and enjoy! (Image 8 above)

Storage, Freezing, and Make Ahead

Storage: Keep leftover cherry cupcakes in an airtight container in the fridge for 3-4 days. Let them come to room temperature before serving!

Freezing: Once filled and frosted, store the cupcakes in an airtight container in the freezer for up to 1 month. They can be defrosted in the fridge overnight.

Make ahead: You can make the cream cheese buttercream 2-3 weeks in advance and keep it in the fridge. The cherry filling can also be made and stored up to 1 week in advance.


What kind of cherries should I use?

I prefer using frozen cherries- they are quicker to cook, and you don’t have to spend time removing the pits! If you have fresh ones on hand, feel free to use them.

How long should I let the cupcakes cool before frosting them?

Allow the cupcakes to cool completely, typically about 1 hour, before frosting to ensure the buttercream doesn’t melt.

Can I use store-bought cherry pie filling?

You can use store-bought cherry filling for convenience, but homemade cherry filling has a fresher flavor!

What is the best way to fill the cupcakes?

After baking and cooling the cupcakes, use a small knife or cupcake corer to remove a portion from the center, then use a piping bag to fill it with the cherry filling.

Can I use all-purpose flour instead of cake flour?

No, cake flour must be used for the best results!

Cherry cupcakes with cherry filling rolled in graham cracker crumbs.

If you tried this or any other recipe on my website, please let me know how it went in the comments; I love hearing from you! Also, please leave a star rating while you’re there! You can also tag me on Instagram or Facebook so I can check it out!

Cherry cheesecake cupcakes cut in half on brown parchment paper.

Cherry Cheesecake Cupcakes

5 from 2 votes

Cherry cheesecake cupcakes– sweet vanilla cupcakes with a graham cracker bottom, filled with fresh cherry filling and frosted with my favorite cream cheese buttercream. They're like little cherry cheesecakes in cupcake form!
Print Recipe Save Recipe Pin Recipe
Prep Time: 3 hours
Cook Time: 20 minutes
Total Time: 3 hours 20 minutes
Course: Dessert
Cuisine: American
Servings: 13 cupcakes
Need Metric Measurements?Use the button options below to toggle between US cups and Metric grams!


Graham Cracker Base

  • 1 cup graham cracker crumbs
  • 3 tablespoons unsalted butter, melted
  • 2 tablespoons granulated sugar

Vanilla Cake Batter

  • 1 1/2 cups cake flour, *See notes below for measuring*
  • 3/4 cup granulated sugar
  • 1 3/4 teaspoons baking powder
  • 1/2 teaspoon fine sea salt
  • 6 tablespoons unsalted butter, room temperature
  • 1/3 cup vegetable oil
  • 1/2 cup whole milk, room temperature
  • 1/2 cup sour cream, room temperature
  • 1 egg, room temperature
  • 1 teaspoon vanilla extract

Cherry Filling

  • 2 1/2 cups frozen sweet red cherries
  • 3 tablespoons granulated sugar
  • 2 teaspoons fresh lemon juice
  • 1 tablespoon cornstarch
  • 1 tablespoon water

Cream Cheese Frosting

  • 3/4 cup unsalted butter, room temperature
  • 6 ounces full-fat cream cheese, cold
  • 2 1/4 cups powdered sugar
  • 1 1/2 tablespoons heavy cream
  • 1 teaspoon vanilla paste or extract
  • Extra fresh cherries, for decorating


Make the Cupcake Batter

  • Line a 12-cup cupcake pan with liners and preheat the oven to 350F/180C.
  • Combine the graham cracker crumbs, sugar, and melted butter. Spoon 1 tablespoon of the graham cracker crumbs into the bottoms of each cupcake liner. Set aside the leftovers for later!
    1 cup (105 g) graham cracker crumbs, 3 tablespoons (42 g) unsalted butter, 2 tablespoons (25 g) granulated sugar
  • Whisk together the flour, sugar, baking powder, and salt into the bowl of a stand mixer. Mix in the butter on low speed until combined, about 2 minutes. Then, add the oil. Mix on low speed for exactly 30 seconds until pasty. Scrape down the bowl.
    1 1/2 cups (180 g) cake flour, 3/4 cup (150 g) granulated sugar, 1 3/4 teaspoons baking powder, 1/2 teaspoon fine sea salt, 6 tablespoons (84 g) unsalted butter, 1/3 cup (65 g) vegetable oil
  • Whisk together the milk, sour cream, egg, and vanilla and pour it into the mixing bowl. Mix on low speed until combined and smooth, scraping down the bowl often.
    1/2 cup (120 g) whole milk, 1/2 cup (113 g) sour cream, 1 (50 g) egg, 1 teaspoon vanilla extract
  • Scoop the batter into the cupcake liners so that each one is roughly 3/4 full. Bake for 20-25 minutes or until the tops bounce back when touched. Let the pan cool on a wire rack. You'll have enough batter for roughly 13-14 cupcakes.

Make the Cherry Filling

  • Combine the cherries, sugar, and lemon juice. Cook over medium heat, mashing frequently, for 15-20 minutes or until the cherries have released their juices, are bubbling, and starting to thicken. Stir in the cornstarch slurry and cook 2 minutes longer, then transfer to a bowl and set aside to cool before using.
    2 1/2 cups (320 g) frozen sweet red cherries, 3 tablespoons (36 g) granulated sugar, 2 teaspoons fresh lemon juice, 1 tablespoon cornstarch, 1 tablespoon water

Make the Cream Cheese Frosting

  • In a stand mixing bowl, cream the butter until fluffy, 1-2 minutes. Mix in the cream cheese on low until just combined. Then, mix in the powdered sugar. When combined, beat on medium-low speed until white and fluffy, about 2-3 minutes. Mix in the heavy cream and vanilla until combined.
    3/4 cup (170 g) unsalted butter, 6 ounces full-fat cream cheese, 2 1/4 cups (270 g) powdered sugar, 1 1/2 tablespoons heavy cream, 1 teaspoon vanilla paste or extract


  • Keep the cupcakes in the cupcake pan and core roughly half of the centers. Use a piping bag or spoon to fill the center with the cherry filling, then pipe the cream cheese frosting around the center. Gently roll the sides of the frosting in the reserved graham cracker crumbs. Fill the center with more cherry filling, then garnish with fresh cherries. Enjoy!
    Extra fresh cherries



*Measure your dry ingredients properly. This is my #1 baking tip! Do not ever scoop a measuring cup into your flour, as this always leads to using too much flour. Instead, use the spoon-level method. This means fluffing the flour first, then spooning it into your measuring cup/spoon. For the BEST results, use a kitchen scale!*
Storage/Freezing: Keep any leftovers in an airtight container in the fridge for 3-4 days or freezer for up to 1 month. Let them come to room temperature before serving!
Serving: 1serving | Calories: 520kcal | Carbohydrates: 55g | Protein: 4g | Fat: 32g | Saturated Fat: 17g | Polyunsaturated Fat: 4g | Monounsaturated Fat: 8g | Trans Fat: 1g | Cholesterol: 83mg | Sodium: 245mg | Potassium: 82mg | Fiber: 1g | Sugar: 40g | Vitamin A: 860IU | Vitamin C: 0.4mg | Calcium: 81mg | Iron: 1mg

The calorie information provided for the recipe is an estimate. The accuracy of the calories listed is not guaranteed.

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Recipe Rating


  1. Christina says:

    Gorgeous! Can’t wait to try them soon5 stars

  2. Best cupcakes ever! Tangy, sweet, with the perfect cherry flavor. Highly recommend!5 stars