There's something irresistibly charming about these bite-sized desserts: sweet, creamy, and bursting with cherry goodness. This Cherry Cheesecake Cupcakes Recipe combines the best of cheesecake and cupcakes into one delightful treat that's perfect for any occasion.

There are seven small cupcakes on a white stand with a wavy edge. Each cupcake has one layer of light creamy cake in red and white striped paper cups. On top of each cake layer is a shiny, deep red cherry topping with whole cherries visible, giving a glossy texture and rich color contrast. The background is a white marbled surface. 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

Whenever I've brought these Cherry Cheesecake Cupcakes to a gathering, they vanish before I even get a second helping. The mix of creamy cheesecake filling with that pop of cherry on top makes them a standout dessert everyone raves about.

Perfect Portion Size: These cupcakes are just the right size for a satisfying dessert without overdoing it.
Easy to Bake: Simple steps mean you can whip these up even if cheesecake isn't your usual thing.
Flavor Combination: The vanilla wafer base, tangy cream cheese, and sweet cherry topping are a match made in heaven.
Great for Any Occasion: From casual family dinners to fancy parties, these cupcakes fit right in.

The image shows several small cheesecakes in white paper cups with red checkered patterns, arranged neatly on a black cooling rack. Each cheesecake has two layers: the bottom layer is smooth and creamy white, while the top layer is a shiny, glossy red cherry topping with whole cherries inside. The cheesecakes fill the paper cups completely, and the black cooling rack contrasts with the white marbled background beneath. photo taken with an iphone --ar 2:3 --v 7

Ingredients & Why They Work

Choosing the right ingredients really makes or breaks these cupcakes. Each plays an essential role to achieve that creamy, smooth texture and a satisfying base that holds it all together. Plus, grabbing fresh cream cheese at room temperature speeds up mixing and smooths the batter.

Flat lay of a neat stack of round golden vanilla wafers, three blocks of smooth cream cheese with clean surfaces, a small white bowl filled with granulated white sugar, four whole brown eggs with clean shells, a small white bowl containing bright yellow fresh lemon juice, and a small white bowl heaped with glossy deep red cherry pie filling, all arranged symmetrically on simple white ceramic dishes 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 create a crunchy, sweet base that contrasts wonderfully with the smooth filling.
Cream cheese: The star of the show—soft and creamy, providing that rich cheesecake flavor.
Sugar: Just enough sweetness to balance the tanginess of the cream cheese and lemon.
Eggs: Help bind the cheesecake mixture and give it structure while baking.
Fresh lemon juice: Adds subtle brightness that cuts through the richness.
Cherry pie filling: Provides a sweet, juicy topping that’s an absolute crowd-pleaser.

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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

I love making these cupcakes my own depending on the season or my mood. You can easily swap out the cherry pie filling for other fruit toppings or add your favorite mix-ins to the batter!

Variation: I sometimes add chopped fresh strawberries or blueberries on top instead of cherry pie filling for a fresh twist.
Diet-Friendly Twist: For a lower sugar version, I reduce the sugar slightly and use fresh fruit in place of pie filling.
Texture Add-Ons: A sprinkle of chopped nuts like pecans or almonds on top adds a lovely crunch that I adore.

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

Step 1: Prepping the Creamy Batter

Start by preheating your oven to 350°F (175°C). Then, using a mixer, blend together your softened cream cheese, sugar, eggs, and fresh lemon juice until the mixture is silky and smooth with no lumps. This step is key for that creamy texture you want in cheesecake cupcakes.

Step 2: Setting Up Your Cupcake Tin

Line your muffin tin with cupcake liners. Place a vanilla wafer at the bottom of each liner—the wafer serves as a simple crust that adds both flavor and structure.

Step 3: Filling and Baking

Fill each cup about three-quarters full with the cream cheese mixture. Because this recipe yields about 30 cupcakes, I find it best to bake one tray at a time to ensure each cupcake bakes evenly. Bake each tray for 20 to 22 minutes. They'll look set but expect the centers to sink slightly as they cool — that's perfectly normal.

Step 4: Cooling and Adding the Cherry Topping

Once baked, let them cool completely. When the cupcakes are at room temperature or chilled, scoop a generous spoonful of cherry pie filling right into the center of each cupcake. This adds that juicy burst of flavor that makes these treats so memorable.

Step 5: Chill Before Serving

Place the cupcakes in the refrigerator for at least an hour before serving. This chilling step helps the cheesecake set up nicely and intensifies the flavors.

Top Tip

I’ve learned that patience here pays off — the cheesecake batter can seem soft when it comes out of the oven, and the centers will sink a bit, but letting them cool fully in the fridge helps them firm up perfectly. Here are some tricks I picked up to get the best results:

Room Temperature Cream Cheese: Using cream cheese that's soft but not melted prevents lumps and creates a smooth filling.
Bake One Tray at a Time: This ensures they bake evenly; overcrowding your oven can cause uneven cooking.
Don’t Overfill: Filling the cupcakes about ¾ full helps prevent overflow and cracking during baking.
Cool Completely Before Adding Topping: Adding cherry filling while warm can cause it to sink or bleed, so let cupcakes cool first.

How to Serve Cherry Cheesecake Cupcakes Recipe

Garnishes

I often top mine with a little fresh mint or a few whole cherries to boost the visual appeal. Some whipped cream piped around the cherries adds elegance if you're serving them at a party.

Side Dishes

These cupcakes pair beautifully with a cup of coffee or tea for an afternoon treat. For a dessert spread, I serve them alongside fresh fruit salads or a light lemon sorbet to complement their richness.

Creative Ways to Present

For birthdays or holidays, I’ve arranged these cupcakes on a tiered platter with fresh flowers or edible glitter for a festive touch. Wrapping them individually in clear cellophane bags tied with ribbon also makes them adorable gifts!

Make Ahead and Storage

Storing Leftovers

I keep leftover cupcakes in an airtight container in the fridge. They stay fresh and creamy for up to 3 days — though I rarely have leftovers that long!

Freezing

You can freeze these by placing them on a tray until firm, then transferring to a freezer-safe container. Thaw overnight in the fridge and add cherry topping fresh before serving for best results.

Reheating

These are best served chilled, but if you prefer a slightly softer texture, let them sit at room temperature for 10-15 minutes. Avoid microwaving, as it can affect the texture of the cheesecake.

Frequently Asked Questions:

Can I use store-bought cheesecake filling for this recipe?

While it's tempting to shortcut, I recommend making the cream cheese batter from scratch for the best texture and flavor. Store-bought fillings often don't bake well in cupcake form.

How do I prevent the centers from sinking too much?

Make sure not to overmix the batter, and avoid opening the oven door while baking. Also, filling the cups about ¾ full helps prevent excessive sinking. A slight sink is normal and doesn’t affect taste.

Can I make these cupcakes vegan or dairy-free?

This recipe relies heavily on cream cheese for the texture and flavor, but you can try vegan cream cheese alternatives. Keep in mind texture and baking times may vary, and the results might differ from the classic version.

What's the best way to serve leftover cupcakes?

Leftover cupcakes are best kept refrigerated and can be enjoyed chilled. Bringing them to room temperature for 15 minutes before serving helps take the chill off and brings out the flavors.

Final Thoughts

These Cherry Cheesecake Cupcakes have become my go-to dessert to impress without stress. The way the creamy filling pairs with the crunchy wafer base and the sweet cherry topping is just magic. I hope you enjoy making and sharing this recipe as much as I do—it really is a crowd-pleaser that brings smiles every time.