Cherry Cheesecake Cupcakes Recipe
If you’re searching for the perfect balance of creamy, fruity, and delightfully handheld, these Cherry Cheesecake Cupcakes truly steal the show. Imagine all the charm of classic cherry cheesecake but with a tender cupcake twist: a crisp graham cracker crust, soft vanilla cake, tangy cream cheese buttercream, and a fresh cherry compote spooned right on top. Every bite is a little bit of summer sunshine, whether you’re hosting a backyard picnic or surprising your family with a special dessert. With their irresistible layers and bold cherry flavor, these gems will have everyone asking for your recipe!

Ingredients You’ll Need
This recipe for Cherry Cheesecake Cupcakes keeps things simple yet utterly delicious. Each ingredient was chosen for the part it plays in perfecting flavor, texture, and color, so be sure to use the freshest you can find for a cupcake that really pops.
- Graham cracker crumbs: The classic base for a cheesecake, these crumbs provide a crunchy, buttery layer that contrasts beautifully with the creamy filling.
- Granulated sugar: Adds just the right amount of sweetness to both the crust and batter, making each bite perfectly balanced.
- Butter (unsalted): Melted for the crust and softened for the batter, butter adds rich flavor and ensures a tender crumb throughout.
- Cake flour: Gives the cupcakes a delicate, pillowy texture that sets them apart from regular cupcakes.
- Baking powder: Aids in rising, making your cupcakes delightfully light.
- Salt: Just a pinch brings out all the other flavors and keeps things from tasting flat.
- Eggs (large): The backbone of your batter, eggs help everything hold together and add lovely richness.
- Vanilla extract: A splash perfumes the cupcakes and frosting, tying everything together with a classic bakery scent.
- Sour cream: This secret ingredient adds a subtle tang and keeps the cupcakes moist, even after chilling.
- Whole milk: Loosens the batter just enough for a soft, tender cake.
- Fresh cherries (pitted): The real showstopper, these offer a juicy, tart filling bursting with color and flavor.
- Lemon juice: A squeeze of lemon brightens the cherry compote and balances sweetness.
- Cornstarch & water: Thickens the cherry topping so it nestles perfectly in each cupcake instead of running off.
- Cream cheese (softened): For a frosting that’s creamy, tangy, and sturdy enough to pipe sky-high.
- Powdered sugar: Melts right into the buttercream for a super-smooth, luscious finish.
- Heavy cream: A final touch to make the frosting extra fluffy and decadent.
How to Make Cherry Cheesecake Cupcakes
Step 1: Prep Your Oven and Tin
Get started by preheating your oven to 350°F (175°C). Line a standard muffin tin with cupcake liners—this not only gives your Cherry Cheesecake Cupcakes that classic bakery look, but also makes them a breeze to remove later on.
Step 2: Build the Graham Cracker Crust
Stir together the graham cracker crumbs, granulated sugar, and melted butter until fully combined. Spoon a heaping tablespoon into each liner, pressing firmly to form a solid crust. Slide the tin into your hot oven and bake for 8 to 10 minutes. The crusts should look set and smell fantastically toasty—let them cool a few minutes while you whip up the batter.
Step 3: Whisk Up the Cupcake Batter
Cream together the softened butter and sugar until the mixture is light and fluffy. Add eggs one at a time, followed by a generous splash of vanilla extract. In a separate bowl, whisk together cake flour, baking powder, and salt. Alternate adding this dry mixture with sour cream and milk, mixing until just combined. The result is a rich, silky batter destined for greatness.
Step 4: Assemble and Bake
Spoon your cake batter evenly over the baked graham cracker crusts, filling each liner about two-thirds full. Bake for 18 to 20 minutes until the tops spring back lightly to the touch (or a toothpick comes out with just a few moist crumbs). Once baked, let the cupcakes cool completely in the tin before adding cherry filling and frosting—patience is key here!
Step 5: Make the Fresh Cherry Filling
In a small saucepan, combine the pitted cherries, sugar, and lemon juice. Heat gently until the cherries start to break down and become syrupy, about 5 minutes. Stir in the cornstarch-water slurry and cook for another minute or two, just until the mixture thickens enough to hold its shape. Let cool before filling the cupcakes—this step is where everything gets super juicy and irresistible.
Step 6: Whip Up the Cream Cheese Buttercream
Beat together the softened cream cheese and butter until completely smooth, scraping the bowl as needed. Gradually add in the powdered sugar, vanilla, and finally the heavy cream. Keep beating until your frosting is luxuriously fluffy and pipeable.
Step 7: Fill and Frost
Once cupcakes and cherry filling are completely cool, cut a small hole in the center of each cupcake (a paring knife or apple corer works wonders). Spoon in a bit of cherry filling, then pipe generous swirls of cream cheese frosting on top. Finish with another dollop of cherry compote and admire your bakery-worthy Cherry Cheesecake Cupcakes!
How to Serve Cherry Cheesecake Cupcakes

Garnishes
The right garnish can take your Cherry Cheesecake Cupcakes from charming to absolutely show-stopping. Try topping each one with a whole cherry, a sprinkle of crushed graham crackers, or even a curl of white chocolate. A little dusting of powdered sugar or a twist of lemon zest brightens up the look and flavor instantly.
Side Dishes
Since these cupcakes are quite rich and fruity, keep your sides light and fresh. Think a big bowl of mixed berries, a zesty fruit salad, or a prettily arranged platter of sliced melons. If you’re serving these for a party, an assortment of iced teas or sparkling lemonade compliments the tangy, creamy goodness beautifully.
Creative Ways to Present
For maximum impact, arrange the Cherry Cheesecake Cupcakes on a simple white cake stand or line them up on a rustic wooden board. Swirl the buttercream high and add edible flowers for a garden party vibe, or display them in mini mason jars for adorable favors. Stack them in a tiered dessert tower for an unforgettable centerpiece!
Make Ahead and Storage
Storing Leftovers
If you have any Cherry Cheesecake Cupcakes left (lucky you!), they’ll keep beautifully for up to three days in the fridge. Be sure to store them in an airtight container to keep the cake moist and prevent the frosting from absorbing fridge odors. Let cupcakes sit at room temperature for 20 minutes before serving for the best flavor and texture.
Freezing
Want to prep ahead? You can freeze the unfrosted cupcakes and cherry filling separately for up to 2 months. To freeze, wrap the cupcakes tightly in plastic wrap and place the filling in a sealed freezer-safe container. Thaw both overnight in the refrigerator before assembling and frosting as usual.
Reheating
While you won’t need to reheat these cupcakes, you can refresh them by letting bake-at-home Cherry Cheesecake Cupcakes come to room temperature for about 30 minutes before serving. Avoid microwaving, as it may cause the frosting to melt and the cake to dry out.
FAQs
Can I use frozen cherries for the filling?
Yes, frozen cherries work just as well as fresh ones. Simply thaw and drain them before cooking with sugar and lemon juice, then proceed as directed. The flavor stays vibrant, and no one will ever know the difference!
Do I really need cake flour, or can I use all-purpose?
Cake flour gives a softer, more tender crumb that really suits these cupcakes. If you’re in a pinch, you can make a substitute by removing 1 tablespoon per cup of all-purpose flour and replacing it with cornstarch. Sift together before using for best results.
How do I core the cupcakes for the cherry filling?
An apple corer or even a small paring knife makes the job easy—just cut out a small circle from the center of each cupcake, then spoon in the filling. Don’t worry about perfection; the frosting will hide any rough edges.
Can I make the cream cheese buttercream ahead of time?
Absolutely! Store your cream cheese frosting tightly covered in the refrigerator for up to three days. Give it a quick beat with a mixer and let it come to room temperature to restore smoothness before piping.
What’s the best way to transport Cherry Cheesecake Cupcakes?
A cupcake carrier or shallow container with a tight lid is your best friend for travel. If it’s a warm day, keep the cupcakes cool with an ice pack underneath to preserve the creamy frosting and cherry filling.
Final Thoughts
If you’re ready to impress yourself and every lucky taster, give these Cherry Cheesecake Cupcakes a try. They’re loaded with flavor, eye-catching, and just plain fun to eat. Once you master this recipe, you’ll find yourself looking for every excuse to bake another batch—enjoy!