Cherry cheesecake cupcakes bring together everything you love about classic cherry cheesecake in a soft, bakery-style cupcake. Each cupcake starts with a buttery graham cracker base, followed by a tender vanilla cake, a bright cherry filling, and a fluffy cream cheese frosting. They are sweet, creamy, fruity, and just a little tangy, making them a beautiful dessert for birthdays, summer parties, holidays, or any time you want a cupcake that feels extra special.
Instead of making a full cheesecake, this recipe gives you the same familiar flavors in a smaller, easier-to-serve form. The graham cracker crumb base adds the cheesecake-style crust, the vanilla cupcake keeps the texture light and soft, and the cherry center gives every bite a juicy burst of fruit. A swirl of cream cheese buttercream finishes the cupcakes with the rich, tangy flavor that makes cheesecake so irresistible.
These cherry cheesecake cupcakes are especially lovely during cherry season, but they can be made year-round with frozen sweet red cherries. Frozen cherries are convenient, easy to cook down into a filling, and do not require pitting. If you prefer a sharper flavor, sour cherries can be used instead. Store-bought cherry pie filling may also be used for convenience, but homemade cherry filling gives the cupcakes a fresher, more balanced taste.
Table of Contents
Tips for Bakery-Style Cupcakes
Measure carefully. For the most consistent cupcakes, use a kitchen scale when possible. Too much flour can make cupcakes dry, dense, or tough. If you are using measuring cups, fluff the flour first, spoon it into the cup, and level it off without packing it down.
Press the graham cracker base firmly. Once the crumbs, sugar, and melted butter are mixed, press the mixture tightly into the bottom of each cupcake liner. The back of a spoon works well. This helps the crust hold together after baking.
Fill the liners evenly. Use a cookie scoop or ice cream scoop to divide the batter. Even portions help the cupcakes bake at the same rate and give them a clean, bakery-style appearance.
Do not overfill the liners. Fill each liner about two-thirds full. Overfilled liners can spill over and make the cupcakes difficult to decorate neatly.
Cool completely before decorating. The cherry filling and cream cheese frosting should not be added while the cupcakes are warm. Warm cupcakes can melt the frosting and make the filling runny.
Core the centers neatly. A cupcake corer, apple corer, or small knife can be used to remove the middle of each cupcake. This creates space for the cherry filling without breaking the cupcake apart.
Ingredient Notes and Substitutions
Frozen sweet red cherries: Frozen cherries are easy to use and cook down into a smooth, flavorful filling. They give the cupcakes a sweet cherry flavor without needing extra preparation. Fresh cherries can also be used if they are pitted first. For a more tart filling, use sour cherries. Cherry pie filling may be used, but it will be sweeter and stronger in flavor.
Cake flour: Cake flour is important for a soft, light cupcake crumb. It gives the batter a more delicate texture than all-purpose flour. For best results, do not substitute it with all-purpose flour, as the cupcakes may become drier and heavier.
Sour cream: Sour cream adds moisture, richness, and tenderness to the vanilla cupcake batter. It also helps the cupcakes stay soft after baking. Full-fat Greek yogurt can be used as a substitute if needed.
Full-fat cream cheese: Brick-style full-fat cream cheese works best for frosting. It creates a thick, creamy, pipeable buttercream. Avoid low-fat cream cheese or cream cheese sold in tubs, because they can make the frosting thin or wet.
Graham cracker crumbs: These create the cheesecake-inspired base and add a buttery crunch beneath the cupcake. Save the extra crumbs after filling the liners so you can use them later for decorating the frosting.
Recipe Instructions
Step 1: Make the graham cracker base. Stir together the graham cracker crumbs, granulated sugar, and melted butter until the mixture resembles wet sand. Add one tablespoon of the crumb mixture to each cupcake liner and press it firmly into the bottom. Set aside any remaining crumbs for decorating later.
Step 2: Combine the dry ingredients. In the bowl of a stand mixer, whisk together the cake flour, sugar, baking powder, and salt. Add the room-temperature butter and mix on low speed until the mixture looks crumbly and evenly combined.
Step 3: Add the wet ingredients. In a separate bowl, whisk together the milk, oil, sour cream, eggs, and vanilla extract. Pour half of this mixture into the dry ingredients and mix until the flour is moistened. Scrape down the bowl, add half of the remaining liquid, mix again, then add the rest and mix just until combined.
Step 4: Bake the cupcakes. Divide the batter between the lined cups, filling each liner about two-thirds full. Bake until the tops spring back when lightly touched. Depending on the size of your pan, you may need to bake the cupcakes in batches.
Step 5: Make the cherry filling. Cook the cherries, sugar, and lemon juice over medium heat, mashing the cherries occasionally as they release their juices. Once the mixture is bubbling and beginning to thicken, stir in the cornstarch slurry. Continue cooking briefly, then transfer the filling to a bowl and let it cool before using.
Step 6: Make the cream cheese frosting. Beat the butter until light and fluffy, then mix in the cold cream cheese on low speed until just combined. Add the powdered sugar and beat on medium-low speed until the frosting is smooth and fluffy. Mix in the heavy cream and vanilla. Avoid beating too quickly, as cream cheese frosting can become thin if overworked.
Step 7: Core and fill the cupcakes. Once the cupcakes are completely cool, remove the center of each one with a cupcake corer, apple corer, or small knife. Spoon or pipe cherry filling into the center of each cupcake.
Step 8: Frost and decorate. Pipe a ring of cream cheese frosting around the cherry-filled center. Gently roll or press the outside edge of the frosting into the reserved graham cracker crumbs. Add more cherry filling on top and garnish with fresh cherries if desired.
Storage, Freezing, and Make Ahead
Storage: Store leftover cherry cheesecake cupcakes in an airtight container for 2 to 3 days. They may also be stored in the refrigerator, although refrigeration can make cupcakes lose some moisture. For the best texture, let chilled cupcakes come to room temperature before serving.
Freezing: Filled and frosted cupcakes can be frozen in an airtight container for up to 1 month. Defrost them in the refrigerator overnight, then allow them to sit at room temperature before serving.
Make ahead: The cream cheese buttercream can be made 2 to 3 weeks in advance and stored in the refrigerator. The cherry filling can be prepared up to 1 week ahead and kept chilled until ready to use.
FAQs
Frozen sweet red cherries are convenient because they cook quickly and do not need to be pitted. Fresh cherries can also be used if you have them available.
Let the cupcakes cool completely before adding the filling and frosting. This usually takes about 1 hour. If the cupcakes are still warm, the buttercream may melt.
Yes, store-bought cherry pie filling can be used for convenience. Homemade cherry filling will taste fresher and less sweet.
After the cupcakes are baked and cooled, remove part of the center with a cupcake corer or small knife. Then spoon or pipe the cherry filling into the opening.
Cake flour is recommended for the best texture. All-purpose flour can make the cupcakes firmer, drier, and less tender.
More Cupcake Recipes
- Hi-hat Oreo cupcakes
- Chocolate turtle cupcakes
- Strawberry crunch cupcakes
- Lemon poppy seed cupcakes
- Rainbow sherbet cupcakes
If you try these cherry cheesecake cupcakes, leave a comment and rating to share how they turned out. Your feedback is always helpful for other bakers.
Cherry Cheesecake Cupcakes
Ingredients
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
- 3/4 cup + 2 tablespoons granulated sugar
- 1 3/4 teaspoons baking powder
- 1/2 teaspoon fine sea salt
- 4 tablespoons unsalted butter, room temperature
- 1/2 cup whole milk, room temperature
- 1/4 cup vegetable oil
- 1/4 cup sour cream, room temperature
- 2 eggs, 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
Instructions
Make the Cupcake Batter
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Line a 12-cup cupcake pan with liners and preheat the oven to 350F/180C.
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Mix the graham cracker crumbs, sugar, and melted butter. Add 1 tablespoon of the mixture to each liner and press firmly into the bottom. Reserve the leftover crumbs for decorating.
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Whisk the cake flour, sugar, baking powder, and salt in the bowl of a stand mixer. Add the butter and mix on low speed for about 2 minutes, until crumbly.
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In another bowl, whisk together the milk, oil, sour cream, eggs, and vanilla. Add the wet mixture in stages, mixing on low speed and scraping down the bowl between additions.
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Fill the cupcake liners about two-thirds full. Bake for 16 to 22 minutes, or until the tops spring back when touched. Cool completely before filling and frosting.
Make the Cherry Filling
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Combine the cherries, sugar, and lemon juice in a saucepan. Cook over medium heat for 15 to 20 minutes, mashing the cherries often, until the juices release and the mixture begins to thicken. Stir the cornstarch and water together, add the slurry to the cherries, and cook for 2 minutes more. Transfer to a bowl and cool before using.
Make the Cream Cheese Frosting
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Beat the butter until fluffy, about 1 to 2 minutes. Mix in the cold cream cheese on low speed until just combined. Add the powdered sugar, then beat on medium-low speed for 2 to 3 minutes, until light and fluffy. Mix in the heavy cream and vanilla.
Assembly
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Core the centers of the cooled cupcakes. Fill each center with cherry filling. Pipe cream cheese frosting around the filling, roll the frosting edges in reserved graham cracker crumbs, and top with more cherry filling. Garnish with fresh cherries if desired.
Notes
Measure dry ingredients properly. For best results, use a kitchen scale. If using cups, spoon the flour into the measuring cup and level it off instead of scooping directly from the bag.
Storage and freezing: Store leftovers in an airtight container in the refrigerator for 3 to 4 days or freeze for up to 1 month. Let the cupcakes come to room temperature before serving.
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Calories: 520 kcal
The calorie information provided is an estimate, and accuracy is not guaranteed.