There's something utterly delightful about these individual treats—the creamy texture, the tangy-sweet burst of cherries, and that nostalgic vanilla wafer base all wrapped into one. This Cherry Cheesecake Cupcakes Recipe truly makes dessert time feel special, whether it's for a casual family night or a festive gathering.

There are seven small desserts placed on a white, wavy-edged cake stand, each in a white paper cup with red checkered and zigzag patterns. Each dessert has three layers: the bottom layer is a light creamy white base, the middle layer is a crumbly crust barely visible inside the cup, and the top layer is a shiny, dark red cherry topping with whole cherry pieces that look juicy and glossy. The background is a white marbled texture with a dark area behind the stand, giving a nice contrast. 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 honestly love how effortlessly this recipe comes together, yet it delivers such a show-stopping dessert. It's one of those cherry cheesecake cupcakes that people immediately ask for seconds on—and with good reason!

Perfect Portion Sizes: Each cupcake is an individual serving, making sharing and storage a breeze.
Simple Ingredients: No complicated steps or weird ingredients, just classics you probably already have.
Beautiful Presentation: Those pools of cherry pie filling on top add eye-catching color and flavor.
Flawless Texture: Creamy cheesecake with a crisp vanilla wafer base—texture lovers, you’re in for a treat!

A group of mini cheesecakes arranged neatly on a black cooling rack over a white marbled surface. Each cheesecake has three visible layers: a smooth, pale yellow base, a thick, creamy white middle layer, and a glossy, vibrant red cherry topping with whole cherries and syrup pooling slightly in the center. All cheesecakes are held in white paper cups with red patterns. The lighting highlights the glossy texture of the cherry topping and the creamy middle layer, creating a fresh and appetizing look. Photo taken with an iphone --ar 2:3 --v 7

Ingredients & Why They Work

Each ingredient in the Cherry Cheesecake Cupcakes Recipe plays a vital role. The cream cheese and eggs give you that classic cheesecake texture, while lemon juice adds a fresh tang to balance the sweetness. And vanilla wafers? They’re not just cute—they add a subtle crunch that keeps every bite interesting.

Flat lay of a small stack of round vanilla wafers with a golden-brown color, three blocks of smooth cream cheese at room temperature with a creamy white texture, a small white ceramic bowl filled with fine white granulated sugar, four whole brown eggs with clean shells, a small white ceramic bowl containing bright yellow fresh lemon juice, and a small white ceramic bowl heaping with glossy, deep red cherry pie filling placed in perfect symmetry 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 buttery, crunchy base that contrasts beautifully with the creamy filling. Use fresh ones for best texture.
Cream cheese: At room temperature, it blends smoothly to create that silky, rich cheesecake body.
Sugar: Sweetens everything without overpowering the natural tang of the cream cheese and lemon.
Eggs: They bind the filling and help it set just right, giving you a firm but creamy cupcake.
Fresh lemon juice: That bright zing really lifts the flavors and keeps things from tasting too heavy.
Cherry pie filling: Adds a luscious, fruity finish and visual pop that’s just irresistible.

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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

While I adore this classic version, I like to play around with flavors a bit depending on the occasion. These cupcakes are versatile, so don't hesitate to make them your own and surprise your taste buds.

Variation: Adding a teaspoon of almond extract to the batter gave these cupcakes a subtle, nutty twist I found lovely and unexpected—definitely a new family favorite.
Dietary tweak: If you're after a lighter version, swapping half the cream cheese with Greek yogurt keeps the creaminess but cuts calories.
Seasonal change: In the summer, I sometimes swap the cherry filling for fresh berries mixed with a splash of lemon juice for a bright, fresh topping.

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

Step 1: Prepping Your Batter

Start by preheating your oven to 350 degrees. Then, with a mixer, blend the softened cream cheese, sugar, eggs, and fresh lemon juice until you get a silky smooth batter. This part is key! Overmixing can cause cracks later, so mix just until combined.

Step 2: Setting the Base

Line a muffin tin with papers and place a vanilla wafer at the bottom of each cup. This wafer gives a sweet crunch base that cuts through the creamy filling—trust me, don't skip it!

Step 3: Filling and Baking

Fill each lined muffin cup about ¾ full with your cheesecake batter. One important thing: bake one tray at a time to ensure even cooking. I’ve learned the hard way that trying to bake multiple trays results in unevenly set cupcakes. Bake each tray for 20 to 22 minutes.

Step 4: Cooling & Adding Cherry Topping

Once baked, let the cupcakes cool completely. You'll notice the centers sink a bit—that’s totally normal and actually perfect for holding the cherry pie filling. Spoon a generous amount of cherry topping into each cupcake’s center, then refrigerate for at least an hour before serving. This chilling helps the flavors marry and the texture firm up beautifully.

Top Tip

From my experience making these cherry cheesecake cupcakes countless times, a few simple tricks make all the difference between good and great.

Room Temperature Ingredients: Make sure your cream cheese and eggs are soft to prevent lumps and achieve a smooth batter.
One Tray at a Time: Baking trays individually ensures they bake evenly and don’t crack from too much heat imbalance.
Watch Your Bake Time: Aim for a slightly jiggly center when you pull them out—the cupcakes will firm up while cooling.
Don't Skip Chilling: Refrigeration is essential for the best texture and flavor, so be patient and give it time.

How to Serve Cherry Cheesecake Cupcakes Recipe

cherry cheesecake cupcakes - Serving Suggestion

Garnishes

I love topping mine with just a simple scoop of cherry pie filling, but you can elevate the look with a dollop of whipped cream or even a sprinkle of toasted almonds for some crunch. It’s all about balancing that sweet-tart cherry with creamy richness!

Side Dishes

These cupcakes pair wonderfully with a light, herbal tea or a fresh coffee. If you want to go all out, try serving with a small bowl of fresh berries or a simple green salad for a refreshing contrast after dessert.

Creative Ways to Present

For a party, I’ve arranged these cupcakes on a tiered stand, adding fresh mint leaves and edible flowers around to create a festive centerpiece. You can also serve them in pretty cupcake liners that match your theme—they’re charming visual gifts that guests appreciate.

Make Ahead and Storage

Storing Leftovers

Once chilled, I store any leftovers in an airtight container in the fridge. They stay fresh and maintain that creamy texture for up to 4 days, perfect for enjoying a sweet treat anytime.

Freezing

If you want to freeze them, I recommend skipping the cherry topping until after thawing. Freeze the plain cheesecake cupcakes in a single layer on a baking sheet, then transfer to a freezer-safe container. They freeze well for about 2 months.

Reheating

To enjoy frozen cupcakes, thaw overnight in the fridge and add cherry topping before serving. If you like them a bit warmer, briefly microwave for 10-15 seconds—but I love them best chilled!

Frequently Asked Questions:

Can I use frozen cherries instead of cherry pie filling?

Frozen cherries can work but I find the pie filling’s syrupy sweetness and texture really finishes the cupcakes perfectly. If you use frozen cherries, mix them with a bit of sugar and cornstarch and cook down to a thick topping first.

Why do the centers of my cheesecakes sink?

It’s totally normal for these cheesecake cupcakes to sink in the middle as they cool—that’s actually a sign they’re perfectly baked and ready for the cherry topping. Avoid overmixing or overbaking to reduce cracking.

Can I make these cupcakes gluten-free?

Absolutely! Use gluten-free vanilla wafers or crushed gluten-free cookies at the base, ensuring all other ingredients are naturally gluten-free. The recipe remains just as delicious!

How long do these cupcakes last in the fridge?

Stored in an airtight container, these cherry cheesecake cupcakes will stay fresh and tasty for up to 4 days. Make sure to keep them chilled, especially because of the cream cheese filling.

Final Thoughts

This Cherry Cheesecake Cupcakes Recipe holds a special place in my collection because it’s such a crowd-pleaser that’s surprisingly easy to make. Whenever I whip these up, I get comments on how decadent they taste despite the simple ingredients. I genuinely hope you enjoy baking and sharing them as much as I do—there’s nothing like the joy of seeing someone’s face light up with that first bite!