Name: Cherry Cheesecake Cupcakes Recipe
Prep time: 10 min
Cook time: 1 h
Total time: 1 h 10 min
Cuisine: American
Ingredients: 30 vanilla wafers; 3 8-ounce packages of cream cheese (at room temperature); 1 cup sugar; 4 eggs; 2 tbsp fresh lemon juice; Cherry pie filling (amount as needed for topping 30 cupcakes)

Imagine biting into a perfectly creamy, tangy cheesecake that fits right into a cupcake liner—plus the surprise of a juicy cherry center. That’s exactly what the Cherry Cheesecake Cupcakes Recipe delivers, blending nostalgic vanilla wafers with luscious cream cheese and bright cherries for a dessert that’s easy to share and hard to resist.

Seven small cheesecakes are displayed on a white scalloped cake stand over a white marbled surface. Each cheesecake is in a white paper cup with red checkered stripes. The cheesecakes have a smooth pale cream base as the first layer, topped with a shiny bright red cherry topping with visible whole cherries creating a slightly uneven texture. The bright red topping contrasts with the creamy base and the patterned paper cups. The 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 serve these cupcakes, they’re the first dessert to vanish. There’s just something about mini cheesecakes that feel special yet approachable, making them perfect for everything from casual get-togethers to holiday celebrations.

Super Simple Prep: The basic ingredients come together quickly without complicated techniques, which means you can whip these up even on a busy day.
Perfect Portion Size: No slicing needed—each cupcake is an individual treat that’s just right for sharing or savoring alone.
That Burst of Cherry Goodness: The cherry pie filling adds a beautiful pop of color and juicy sweetness that balances the creamy tang of the cheesecake.
Classic Meets Comfort: Layering vanilla wafers at the base gives a nostalgic crunch that’s both fun and comforting, reminding me of family dessert traditions.

The image shows many mini cheesecakes placed closely on a black wire rack over a white marbled surface. Each cheesecake has three clear layers: a white creamy base filling the cupcake liners that are white with red zigzag patterns, topped by a shiny, bright red cherry topping with visible cherry pieces. The red topping looks glossy and slightly thick, contrasting with the smooth white cheesecake below. The cupcakes are arranged in neat rows, filling the frame with a sense of abundance. photo taken with an iphone --ar 2:3 --v 7

Ingredients & Why They Work

Each ingredient is a star here, working together to create creamy, tangy, and sweet harmony. Plus, these are items you can likely grab from your pantry or local store without a headache.

Flat lay of a neat stack of round vanilla wafers, three blocks of smooth cream cheese with clean edges, a small white bowl filled with granulated white sugar, four whole brown eggs with clean shells, a small white bowl holding fresh lemon juice with a pale yellow hue, and a small white bowl heaped with glossy bright red cherry pie filling, all arranged symmetrically and balanced 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 add a lovely crunchy base—think of them as mini crusts that keep each cupcake stable and tasty.
Cream cheese: The heart of that dreamy texture; make sure it’s softened for smooth mixing and silky cupcakes.
Sugar: Sweetens just enough without overpowering the tang from the cream cheese and lemon.
Eggs: Provide structure and richness that hold the cupcakes together while keeping them moist.
Fresh lemon juice: A splash of brightness that cuts through the richness, adding a refreshing zing.
Cherry pie filling: The crowning touch that adds natural sweetness and a beautiful jewel-toned surprise inside each cupcake.

📝

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 tweaking this Cherry Cheesecake Cupcakes Recipe depending on the season or mood—sometimes adding a splash of almond extract or swapping cherry filling for raspberry or blueberry. You should definitely experiment and find what suits your taste!

Variation: One fall, I tried adding a sprinkle of cinnamon and nutmeg to the batter—it gave a cozy twist that everyone enjoyed, especially paired with a cup of hot tea.
Dairy-free option: Try vegan cream cheese and egg substitutes to keep this recipe inclusive while still capturing that creamy essence.
Mini cheesecake bites: Use a mini muffin tin for smaller portions that are ideal for parties or kids’ lunchboxes.

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

Step 1: Prep like a pro

Preheat your oven to 350 degrees and line your muffin tin with cupcake liners. Having everything ready means you’ll breeze through the baking process without scrambling, and the liners keep clean-up easy.

Step 2: Mix till creamy

Using a mixer, blend your softened cream cheese, sugar, eggs, and lemon juice until the batter is smooth and silky. Don’t rush this step—it makes all the difference for a velvety texture and no lumps.

Step 3: Layer and fill

Place a vanilla wafer at the bottom of each muffin cup. This acts like the classic cheesecake crust but in miniature form. Then, fill each cup about ¾ full with your cream cheese mixture. Don’t overfill to avoid spills during baking.

Step 4: Bake carefully

Bake each tray separately for 20-22 minutes—baking one tray at a time helps them cook evenly. You’ll notice the centers sink slightly when they cool down, but that’s exactly what you want for the perfect nest to hold the cherry topping.

Step 5: Add the cherry finishing touch

Once cooled, gently scoop a spoonful of cherry pie filling right into the sunken center of each cupcake. Resist the urge to add too much or it might spill over, but a generous scoop adds stunning color and flavor contrast.

Step 6: Chill and serve

Pop the cupcakes in the fridge for at least an hour. This step lets the flavors meld and ensures a firm, luscious texture when you bite in. The wait is always worth it!

Top Tip

I’ve made these Cherry Cheesecake Cupcakes Recipe countless times, and a few little tweaks really make them shine. Here’s what I’ve learned so you don’t have to stress in the kitchen like I did initially!

Use room temperature cream cheese: It blends effortlessly with other ingredients, giving you a perfectly smooth batter without lumps.
Bake trays separately: I used to bake multiple pans at once, but uneven cooking was a problem—baking one tray at a time guarantees consistency.
Don’t skip the chill: Refrigerating firm-ups the cupcakes and highlights the tangy flavor; trust me, serving these warm just doesn’t do them justice.
Choose good quality cherry pie filling: I’ve found that the filling really makes or breaks the dessert, so pick one with whole or large cherry pieces for that perfect juicy finish.

How to Serve Cherry Cheesecake Cupcakes Recipe

cherry cheesecake cupcakes - Serving Suggestion

Garnishes

I usually keep it simple with a dusting of powdered sugar or a few fresh cherries on top to amp up the presentation. Sometimes whipped cream or a sprinkle of toasted almonds adds a lovely texture contrast if I’m feeling fancy.

Side Dishes

These cupcakes pair perfectly with a light dessert wine or a hot cup of coffee or tea. If your event calls for more, a fresh fruit salad or simple vanilla ice cream complements the richness beautifully.

Creative Ways to Present

For celebrations, I’ve assembled them on tiered stands or served them in decorative cupcake boxes for gifting. Layered with festive ribbons or little edible flowers, they instantly become a showstopper on any dessert table.

Make Ahead and Storage

Storing Leftovers

Store your Cherry Cheesecake Cupcakes in an airtight container in the fridge. They stay fresh and creamy for up to 4 days, though they rarely last that long in my house!

Freezing

I’ve frozen these cupcakes without the cherry topping before. Just wrap them well and stash in a freezer-safe container. When ready, thaw overnight in the fridge and add fresh cherry pie filling before serving for best results.

Reheating

Since these are best served chilled, I don’t recommend reheating. Instead, enjoy them cold or let them sit at room temperature for 10 minutes if your fridge made them too firm.

Frequently Asked Questions:

Can I make these cupcakes ahead of time?

Absolutely! You can bake them a day or two in advance, keep them refrigerated, and add the cherry pie filling just before serving to keep that fresh burst of flavor.

Can I use frozen cherries instead of cherry pie filling?

You can, but you’ll want to make a simple cherry topping by cooking frozen cherries with a bit of sugar and cornstarch to thicken it up. The pre-made pie filling is more convenient and has the right sweetness and texture.

Why do the centers of the cupcakes sink?

That’s totally normal for cheesecake-style cupcakes because of the soft cream cheese batter and how it sets while cooling. The sunken center actually makes a perfect little pocket for the cherry topping.

Can I make this recipe gluten-free?

Definitely! Use gluten-free vanilla wafers for the base, and just be sure your cherry pie filling is gluten-free as well. The rest of the recipe is naturally gluten-free.

Final Thoughts

This Cherry Cheesecake Cupcakes Recipe has become one of my go-to desserts for any occasion—it’s reliable, crowd-pleasing, and just downright delicious. I hope you enjoy making and eating it as much as I do, creating sweet moments one cupcake at a time. Give it a try and make it your own—you might just end up sharing this recipe for years, like I have!