There’s something so irresistible about the blend of creamy cheesecake and sweet cherries nestled in a perfectly portioned treat. This Cherry Cheesecake Cupcakes Recipe combines all those delightful flavors into easily shareable, adorable cupcakes — a dessert that’s as fun to make as it is to eat.

Seven small cheesecakes in white cupcake liners with red stripes, placed on a white ceramic cake stand with wavy edges. Each cheesecake has three visible layers: a pale beige crust base at the bottom, a smooth and creamy white cheesecake layer in the middle, and a glossy bright red cherry topping made of whole cherries and syrup on the top. The cake stand is set on a white marbled surface. 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

This recipe quickly became one of my go-tos for gatherings because it feels fancy but is downright simple. The cupcakes have this perfect balance of textures and flavors that keep everyone coming back for seconds — and sometimes thirds!

Easy to share: These individual cupcakes are perfect for potlucks or parties — no cutting required.
Satisfyingly creamy: The cream cheese batter creates a smooth cheesecake filling that melts in your mouth.
Bright cherry topping: A luscious cherry pie filling adds a pop of color and sweet-tart flavor that elevates every bite.
Minimal ingredients: With pantry staples plus a few fresh additions, it’s straightforward enough for even a newbie baker.

There are many small cheesecake cups arranged in rows on a black cooling rack placed on a white marbled surface. Each cheesecake cup has three visible layers: the bottom is a thin, lighter layer of crust inside a white cupcake liner with red patterns, the middle is a thick, smooth, creamy white cheesecake layer, and the top is a bright red, glossy cherry topping with whole cherries covered in syrup. The cheesecake cups are uniformly placed, creating a neat grid pattern. photo taken with an iphone --ar 2:3 --v 7

Ingredients & Why They Work

Each ingredient plays its role in creating the texture and flavor we crave in these Cherry Cheesecake Cupcakes. I love that you can find almost everything at your local grocery store, making it a last-minute crowd-pleaser.

Flat lay of a stack of round, golden vanilla wafers, three blocks of smooth cream cheese with a creamy white texture, 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 dark red cherry pie filling, all arranged symmetrically on a simple white ceramic surface, 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: Form a crisp, buttery base layer that adds a little crunch and classic vanilla flavor.
Cream cheese: The heart of the cheesecake filling, delivering that rich and creamy profile you expect.
Sugar: Sweetens perfectly without overpowering the tang of the cream cheese and lemon.
Eggs: Bind the filling together smoothly, ensuring a firm yet tender cupcake.
Fresh lemon juice: Adds a subtle brightness that cuts through the richness and lifts the flavor.
Cherry pie filling: The crowning glory — sweet, juicy, and bursting with fruity goodness that contrasts beautifully with the creamy filling.

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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 things I enjoy most about this Cherry Cheesecake Cupcakes Recipe is how easy it is to put your own spin on it. Personally, I’ve tried swapping out the cherry topping for fresh berries or marmalade depending on the season, and it’s always a hit.

Variation: When I wanted a bit more texture, I stirred in chopped toasted almonds into the cream cheese batter — so good!
Dietary tweaks: For a lighter take, you can try reduced-fat cream cheese, but just watch that the texture stays creamy.
Flavor swaps: Another favorite variation is swapping lemon juice with orange zest and juice for a citrus twist.
Make it mini: Bite-sized versions baked in mini muffin tins are perfect for party trays or kids’ lunches.

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

Step 1: Prepping the Batter

Start by preheating your oven to 350°F (175°C). Then, grab your mixer and blend together the softened cream cheese, sugar, eggs, and fresh lemon juice until the mixture’s silky smooth — no lumps! Make sure your cream cheese is at room temperature before mixing; it helps avoid a grainy texture.

Step 2: Assembling the Cupcakes

Place a vanilla wafer at the bottom of each muffin cup — this little touch adds a lovely crunch base. Then, pour in the cream cheese batter, filling about three-quarters full so they have room to rise without overflowing. Remember, the recipe makes about 30 cupcakes, so unless you have multiple pans, baking one tray at a time is best for even cooking.

Step 3: Baking and Cooling

Bake for 20 to 22 minutes and then let them cool on a wire rack. Don’t be alarmed if the centers sink a bit — this is totally normal and gives you the perfect little well for your cherry topping later on.

Step 4: The Cherry Finish

Once cooled, spoon a generous scoop of cherry pie filling right into the sunken center of each cupcake. Pop them into the fridge for at least an hour before serving — chilling helps the flavors to meld and the cupcakes to firm up so they hold their shape beautifully.

Top Tip

After making these cupcakes multiple times, I’ve learned a few little tricks that really make a difference. Trust me on these; they’ll help you nail the perfect cheesecake texture and stunning presentation.

Room temperature cream cheese: No skipping this step—it’s key for a smooth batter. Cold cream cheese makes lumps and a grainy batter.
Bake one tray at a time: It might feel slow, but this ensures that all cupcakes cook evenly without burning or underbaking.
Don’t worry about sinking centers: This is normal for cheesecake cupcakes and actually helps hold your cherry topping.
Chill before serving: Cooling solidifies the texture and the flavors become much more pronounced.

How to Serve Cherry Cheesecake Cupcakes Recipe

Garnishes

I usually keep it simple with just the cherry pie filling right on top, but if I’m feeling fancy, I add a little dollop of whipped cream or a sprinkle of finely chopped toasted pistachios for texture and color. Fresh mint leaves add an elegant touch and a hint of freshness.

Side Dishes

These cupcakes are a dessert star on their own, but I love pairing them with a cup of bold coffee or a light sparkling wine at celebrations. For a full dessert spread, they go beautifully alongside fresh fruit salad or a simple vanilla bean panna cotta.

Creative Ways to Present

For special occasions, I’ve arranged the cupcakes on a tiered stand lined with fresh cherries and edible flowers — it makes for an irresistible centerpiece. You can also serve them in clear cupcake wrappers to show off those beautiful cherry centers.

Make Ahead and Storage

Storing Leftovers

I keep leftovers stored in an airtight container in the fridge, and they stay delicious for up to 4 days. Because of the cream cheese filling, refrigeration is essential to keep them fresh and safe.

Freezing

I've frozen these cupcakes successfully by wrapping each one individually in plastic wrap and placing them all in a freezer-safe container. When you're ready to enjoy, just thaw them overnight in the fridge — they nearly taste freshly baked!

Reheating

I typically avoid reheating to preserve the texture and flavor, but if you want to warm them slightly, a quick 10-second zap in the microwave softens them up without melting the cherry topping.

Frequently Asked Questions:

Can I use frozen cherries instead of cherry pie filling?

While frozen cherries can work, cherry pie filling has added sugar and thickener which creates that perfect glossy topping and sweet flavor. If you use frozen cherries, consider simmering them with some sugar and cornstarch to mimic that texture.

Why do the centers of the cupcakes sink during cooling?

This is typical for cheesecake-style cupcakes because the center sets more softly and contracts as it cools. It’s not a flaw—in fact, it creates a perfect little well for the cherry topping to sit in nicely.

Can I make these cupcakes ahead for a party?

Absolutely! These cupcakes actually taste better after they’ve chilled for several hours or overnight, so making them the day before your event is a great plan. Just keep them refrigerated until serving time.

Do I need to use fresh lemon juice or is bottled lemon juice okay?

Fresh lemon juice definitely brightens the flavor and gives a fresher taste, but bottled lemon juice works in a pinch. Just avoid lemon concentrates or powders—fresh or pure juice delivers the best result.

Final Thoughts

This Cherry Cheesecake Cupcakes Recipe is a little slice of joy I love to share with friends and family. It’s approachable enough for busy days but special enough for celebrations. You’ll enjoy how that burst of cherry sweetness complements the creamy, tangy cheesecake—trust me, once you try these, they might just become your new favorite dessert.