There’s just something so delightful about a dessert that combines creamy cheesecake with a burst of fruity cherry sweetness. These Cherry Cheesecake Cupcakes Recipe bring that magic into perfectly portioned, adorable little treats that everyone will love. Trust me, once you try them, they’ll become a staple for any get-together or just a cozy weekend indulgence.

Seven mini cheesecakes sit arranged on a white wavy plate on a white marbled surface. Each cheesecake has a red and white checkered paper liner holding a smooth, pale cream layer topped with a glossy, thick cherry red topping with visible whole cherries. The red cherry topping contrasts with the light cheesecake layer beneath. 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

I’m genuinely excited to share this Cherry Cheesecake Cupcakes Recipe because it’s one of those desserts that never fails to impress, no matter the occasion. Each cupcake offers that perfect balance of creamy, tangy cheesecake and sweet cherries on a crisp vanilla wafer base—pure bliss in your mouth.

Perfectly Portable: These cupcakes are bite-sized cheesecakes, making them great for parties, picnics, or grab-and-go treats.
Simplicity Meets Elegance: You don’t need fancy tools or complicated steps, but the results taste like you put in a ton of effort.
Made from Everyday Ingredients: You’ll likely have everything you need on hand, so it’s great for last-minute dessert plans.
Customizable: From the type of cherry pie filling to tweaks in the crust, you can make these uniquely yours.

The image shows many small cheesecakes in white paper cups with red patterns, arranged neatly on a black wire cooling rack over a white marbled surface. Each cheesecake has two clear layers: the bottom layer is creamy white and smooth, filling most of the cup, while the top layer is a bright, glossy red cherry topping with whole cherries visible inside. The cherry topping is slightly uneven and shiny, peeking over the edge of the creamy base, and the paper cups create a textured, ruffled border around each cheesecake. photo taken with an iphone --ar 2:3 --v 7

Ingredients & Why They Work

The ingredients in this Cherry Cheesecake Cupcakes Recipe work beautifully together to create layers of texture and flavor. The vanilla wafers form a crisp crust, the cream cheese mixture is luxuriously smooth and tangy, and the cherry pie filling adds that bright, juicy finish. Here’s a quick rundown of why each ingredient matters:

Flat lay of a small stack of round vanilla wafers, three blocks of smooth cream cheese at room temperature, a white ceramic bowl filled with granulated sugar, four whole brown eggs with clean shells, a small white bowl of fresh lemon juice, and a small white bowl with glossy cherry pie filling, all arranged symmetrically 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 simple yet delicious base that holds the cheesecake filling and adds a subtle vanilla crunch.
Cream Cheese: The star of the cheesecake, it gives that rich, creamy texture and tangy flavor.
Sugar: Sweetens the cheesecake batter to balance the cream cheese’s natural tartness.
Eggs: Help set the cheesecake batter while keeping it smooth and creamy.
Fresh Lemon Juice: Adds brightness and cuts through the richness with a subtle citrus note.
Cherry Pie Filling: The fruity topping that adds sweetness, color, and a burst of flavor on each cupcake.

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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 that this Cherry Cheesecake Cupcakes Recipe is so easy to tweak. Over time, I’ve found that a few little twists can really elevate the final treat—so don’t hesitate to make it your own!

Variation: Sometimes I swap the cherry pie filling for blueberry or raspberry preserves, which offers a fresh spin that’s equally delicious and pretty.
Dairy-Free Option: You can experiment with dairy-free cream cheese alternatives, though the texture might be slightly different. Just be sure to check brand consistency.
Extra Crunch: For a fun contrast, I occasionally crumble some buttered graham crackers on top before baking instead of vanilla wafers for a different crust flavor.

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

Step 1: Prepping the Creamy Cheesecake Batter

First things first, preheat your oven to 350°F (175°C). Then, grab your mixer and beat together the cream cheese, sugar, eggs, and fresh lemon juice until everything is smooth and silky. This step is key for the silky texture—make sure there are no lumps! Set the batter aside while you prepare the muffin tin.

Step 2: Assembling Your Cupcakes

Line a standard muffin tin with cupcake liners. This makes cleanup easier and gives the cupcakes a polished look. Place one vanilla wafer at the bottom of each cup—this will add that delicious, crisp base. Then, carefully fill each cup about three-quarters full with the cheesecake batter. Don’t overfill or they’ll spill over as they bake.

Step 3: Baking One Tray at a Time

This recipe yields around 30 cupcakes, but here’s a little trick I learned: bake them one tray at a time. This way they bake evenly and come out perfectly creamy, not overdone. Bake each tray for about 20 to 22 minutes. You’ll notice the centers may sink a bit once they cool — that’s totally normal and actually what creates the perfect little well for the cherry topping.

Step 4: Adding the Cherry Topping and Chilling

After the cupcakes have cooled completely, gently spoon a scoop of cherry pie filling right into the center of each one. This is the grand finale that makes these cupcakes pop with flavor and color. Pop the tray into the fridge for at least an hour before serving so they set beautifully and taste their best.

Top Tip

From my experience making these cupcakes several times, I’ve nailed down a few tips that really help you get the best results — whether it’s your first time or you’re tweaking it for a special occasion.

Room Temperature Cream Cheese: Make sure your cream cheese is softened to room temp; it blends smoothly and prevents lumps in your batter.
Bake in Batches: Baking one tray at a time ensures even cooking — overcrowding your oven can lead to wonky cupcakes.
Don’t Overmix: Once the eggs are incorporated, stop mixing to keep the batter light and avoid cracks.
Use Quality Cherry Filling: The cherry topping is the star, so invest in a good flavor-rich pie filling or homemade cherry compote for extra wow factor.

How to Serve Cherry Cheesecake Cupcakes Recipe

cherry cheesecake cupcakes - Serving Suggestion

Garnishes

When I serve these cupcakes, I like to add a small dollop of whipped cream on top of the cherry filling for some extra creaminess and a pretty finish. A light sprinkle of toasted almond slivers is something I sometimes do for crunch and a touch of elegance—it’s simple but makes them feel special.

Side Dishes

These cupcakes pair wonderfully with a cup of strong coffee or a light, fruity beverage like sparkling lemonade. For a casual dessert spread, I serve them alongside fresh berries or a simple fruit salad to balance the richness.

Creative Ways to Present

For holidays or parties, I’ve arranged these cupcakes on a tiered platter surrounded by edible flowers or fresh mint leaves. Layering them with complementary treats like mini tarts or macaroons turns your dessert table into a stunning spread that guests always comment on.

Make Ahead and Storage

Storing Leftovers

Store any leftovers in an airtight container in the refrigerator. Because of the cream cheese and cherry topping, they’ll keep well for about 3-4 days. I always recommend keeping them chilled until just before serving so they retain their perfect texture.

Freezing

These cupcakes freeze pretty well! When I freeze them, I place them on a tray lined with parchment paper and freeze until firm, then transfer them to a freezer-safe container. When you’re ready to enjoy, thaw them overnight in the fridge to keep the texture intact.

Reheating

I typically don’t reheat cheesecake cupcakes because they're best served chilled. But if you want a slightly softer texture after refrigeration, letting them sit at room temperature for 15–20 minutes before eating works beautifully.

Frequently Asked Questions:

Can I use other types of pie filling instead of cherry?

Absolutely! Blueberry, raspberry, or even peach pie fillings work wonderfully and give you a chance to customize based on your favorite flavors or what’s in season.

Why do the cheesecake cupcake centers sink after baking?

This is totally normal and happens because the batter cools and settles. It actually creates a perfect well to add the cherry pie filling, so don’t worry—it’s part of what makes these cupcakes special.

Can I make these without vanilla wafers?

Yes, you can experiment with graham crackers, crushed cookies, or even a traditional cheesecake crust mix. Just make sure whatever you use is sturdy enough to support the filling.

How do I avoid cracking on the cheesecake topping?

The key is not to overmix your batter and to bake at a moderate temperature. Also, letting the cupcakes cool gradually rather than rushing them helps prevent cracks. Baking one tray at a time ensures even heat distribution, too.

Final Thoughts

Making these Cherry Cheesecake Cupcakes Recipe feels like a little gift to yourself and your loved ones. They’re simple, elegant, and just downright delicious. I hope you enjoy baking them as much as I do, and more importantly, enjoy every creamy, cherry-topped bite. Go ahead, try it out—you’re going to impress everyone and might find yourself making them again and again!