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!
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 (hello cherry season!) 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.
Evenly fill the cupcake liners. Use an ice cream or cookie scoop to distribute the batter into the cupcake liners. 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
Frozen sweet red cherries: 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: For a super light and tender texture, this recipe uses cake flour and 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! Substitute with full-fat Greek yogurt if needed.
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)
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)
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.
FAQs
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.
Allow the cupcakes to cool completely, typically about 1 hour, before frosting to ensure the buttercream doesn’t melt.
Yes, you can use store-bought cherry filling for convenience, but homemade cherry filling has a fresher flavor!
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.
No, cake flour must be used for the best results!
More Cupcake Recipes
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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 *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
Instructions
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 graham cracker crumbs, 3 tablespoons unsalted butter, 2 tablespoons 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 cake flour, 3/4 cup granulated sugar, 1 3/4 teaspoons baking powder, 1/2 teaspoon fine sea salt, 6 tablespoons unsalted butter, 1/3 cup 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 whole milk, 1/2 cup sour cream, 1 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 frozen sweet red cherries, 3 tablespoons 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 unsalted butter, 6 ounces full-fat cream cheese, 2 1/4 cups powdered sugar, 1 1/2 tablespoons heavy cream, 1 teaspoon vanilla paste or extract
Assembly
- 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
Video
Notes
Nutrition
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