There's something irresistibly charming about individual desserts that pack a punch of flavor and nostalgia. This Cherry Cheesecake Cupcakes Recipe combines the creamy richness of cheesecake with the bright sweetness of cherries – all in a perfectly bite-sized treat that’s a joy to make and share.

Seven small cheesecake cups sit on a white cake stand with a scalloped edge, each cheesecake resting in a white paper cup with red checkered patterns. Each cheesecake has two visible layers: the bottom layer is pale cream, smooth and firm, while the top layer is a glossy, deep red cherry topping with whole cherries, shiny and thick, piled in the center. The background has a white marbled texture. photo taken with an iphone --ar 2:3 --v 7

Jump to:

Why You'll Love This Recipe
Ingredients & Why They Work
Make It Your Way
Step-by-Step: How I Make Cherry Cheesecake Cupcakes Recipe
Top Tip
How to Serve Cherry Cheesecake Cupcakes Recipe
Make Ahead and Storage
Frequently Asked Questions:
Final Thoughts
Cherry Cheesecake Cupcakes Recipe

Why You'll Love This Recipe

I adore this Cherry Cheesecake Cupcakes Recipe because it’s wonderfully straightforward but feels special enough for any occasion. Whether it’s a casual weekend treat or a party showstopper, these cupcakes strike a perfect balance of creamy and fruity that always wins hearts.

Simple Ingredient List: You'll find everyday pantry staples come together to create something extraordinary.
Perfect Portioned Treats: Individual cupcakes that are easy to serve and even easier to enjoy without any fuss.
Beautiful Presentation: That pop of cherry pie filling on top makes these cupcakes look like you spent hours on dessert.
Customizable Flavor: You can tweak the lemon juice, choose different fruit toppings, or even swap the vanilla wafers for something else to suit your taste.

The image shows many small cheesecake cups arranged on a black wire cooling rack over a white marbled surface. Each cheesecake cup has three layers: the bottom layer is a light beige crust, the middle layer is smooth white cheesecake filling, and the top layer is a shiny red cherry topping with whole cherries visible. The cups are in white paper liners decorated with red zigzag patterns, adding a festive look to the dessert. The scene is brightly lit, showing the gloss on the cherry topping clearly. photo taken with an iphone --ar 2:3 --v 7

Ingredients & Why They Work

The magic of this recipe lies in the harmony between creamy, crunchy, and fruity. Each ingredient plays its part to build that perfect cheesecake cupcake experience—nothing complicated, just good, honest ingredients that complement each other beautifully.

Flat lay of a stack of round vanilla wafers, three blocks of cream cheese with smooth surfaces, a small white bowl of granulated sugar, four whole brown eggs with clean shells, a small white bowl of bright yellow fresh lemon juice, and a small white bowl filled with glossy deep red cherry pie filling, arranged with perfect symmetry on a simple white ceramic plate and bowls, placed on a clean white marble surface, soft natural light, photo taken with an iPhone, professional food photography style, fresh ingredients, white ceramic bowls, no bottles, no duplicates, no utensils, no packaging --ar 2:3 --v 7 --p m7354615311229779997

Vanilla Wafers: These form a sweet, crisp base which is a fun alternative to a traditional graham cracker crust.
Cream Cheese: Make sure it's at room temperature for the smoothest batter and best texture.
Sugar: Sweetens the cheesecake filling without overpowering it.
Eggs: These bind everything together and give the cupcakes structure.
Fresh Lemon Juice: Adds a subtle tang that brightens the rich cream cheese beautifully.
Cherry Pie Filling: The crowning glory—sweet cherries soaked in syrup add both flavor and visual appeal.

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Note: You'll find the complete list of ingredients, along with their exact measurements, in the printable recipe card at the bottom of this post.

Make It Your Way

One of the best parts about this Cherry Cheesecake Cupcakes Recipe is how easy it is to adjust for your personal preferences or whatever you have on hand. I like to add a little vanilla extract for an extra flavor kick, but you could also experiment with different fruit toppings or even a sprinkle of nuts on top for crunch.

Variation: I once swapped out the cherry pie filling for blueberry preserves. It was a hit at a summer picnic, giving it a fresh, seasonally fruity twist.
Dietary Modification: For a lighter version, try using low-fat cream cheese, though the texture will be a bit less silky.
Presentation: Sometimes I dust the cooled cupcakes with powdered sugar for a delicate finish before adding the cherry topping.

Step-by-Step: How I Make Cherry Cheesecake Cupcakes Recipe

Step 1: Bring Your Ingredients to Room Temperature

This is key! Make sure your cream cheese and eggs aren’t cold straight from the fridge. Room temperature ingredients blend smoother, which helps avoid lumps and gives you that silky cheesecake texture.

Step 2: Create the Cream Cheese Batter

Using a mixer, beat together the cream cheese, sugar, eggs, and fresh lemon juice until you get a perfectly smooth batter. Don't rush this part – scraping down the sides a couple of times ensures everything is well incorporated.

Step 3: Prepare the Muffin Tin

Line your muffin tin with sturdy paper liners. Drop a vanilla wafer into the bottom of each cup — these little wafers add a lovely crunch and sweetness as a base for each cupcake.

Step 4: Fill and Bake the Cupcakes

Carefully fill each lined cup about three-quarters full with the cheesecake batter. Bake one tray at a time at 350°F (175°C) for 20–22 minutes. This approach helps them bake evenly and prevents soggy or undercooked centers.

Step 5: Cool and Top with Cherries

Let the cupcakes cool completely — they’ll sink a little in the center, which is perfect because that’s where the cherry pie filling goes. Spoon a generous scoop of cherries on top of each cooled cupcake, then refrigerate for at least an hour before serving.

Top Tip

From my experience making these Cherry Cheesecake Cupcakes Recipe multiple times, I’ve learned a few little tricks that make all the difference between good and spectacular.

Room Temperature Ingredients: This ensures the batter blends perfectly smooth, avoiding lumps and creating a better texture.
Don’t Overbake: Watch the baking time closely; it can vary by oven. The edges should be set but the center may still jiggle slightly, which is just right.
One Tray at a Time: Baking one tin at a time helps with even cooking, preventing burnt edges and undercooked middles.
Add Toppings After Cooling: Placing the cherry filling on cooled cupcakes keeps its texture intact and prevents it from sinking or getting watery.

How to Serve Cherry Cheesecake Cupcakes Recipe

Garnishes

I love topping mine with a little extra fresh cherry for that natural brightness and a light dusting of powdered sugar before serving. Sometimes a small sprig of mint adds a nice fresh contrast to the rich cheesecake flavor.

Side Dishes

When serving these cupcakes, I like pairing them with a cup of rich, dark coffee or a tart herbal tea to balance the sweetness. For a party spread, fresh fruit salad or a light whipped cream complements these cupcakes well without overwhelming the flavors.

Creative Ways to Present

For special occasions, I arrange the cupcakes on a tiered dessert stand with decorative paper liners and add a few whole cherries around the base. Another fun idea is to place each cupcake in a small clear treat bag tied with a ribbon – perfect for gifting or party favors.

Make Ahead and Storage

Storing Leftovers

I keep leftover Cherry Cheesecake Cupcakes refrigerated in an airtight container to maintain freshness. They usually stay perfectly delicious for about 3-4 days, though they rarely last that long in my house!

Freezing

You can freeze these cupcakes before adding the cherry topping. Wrap each one individually in plastic wrap, then place in a freezer-safe container. When you’re ready, thaw in the fridge overnight, add cherry pie filling, and enjoy.

Reheating

I typically enjoy these chilled, but if you want to warm them up, pop a cupcake in the microwave for about 10 seconds—just enough to take the chill off without compromising texture.

Frequently Asked Questions:

Can I use store-bought cheesecake filling instead of making the batter?

While store-bought cheesecake filling might seem like a shortcut, it’s often too thick or sweet for this recipe’s texture. Making the batter fresh ensures the perfect balance and smoothness.

Why do the centers of the cupcakes sink after baking?

It’s normal! The centers will slightly sink because of the cream cheese and eggs. This actually creates a perfect little well for the cherry pie filling.

Can I substitute a different fruit for the cherry pie filling?

Absolutely! Blueberry, raspberry, or even strawberry pie filling works wonderfully. Just choose what you and your family love best.

How should I store leftover Cherry Cheesecake Cupcakes?

Store them in an airtight container in the refrigerator. They keep well for about 3-4 days, but always best to enjoy sooner for maximum freshness and flavor.

Final Thoughts

These Cherry Cheesecake Cupcakes hold a special spot in my recipe collection because they’re approachable yet feel indulgent—like little celebrations in cupcake form. I’m confident you’ll enjoy making them as much as I do. So next time you want to delight your friends or family with something charming and delicious, give this recipe a try. I promise they’ll be asking for seconds!