There’s something delightfully nostalgic and fresh about these little treats, and that’s exactly why I’m excited to share this Cherry Cheesecake Cupcakes Recipe with you. Combining creamy cheesecake goodness with a burst of cherry, each bite feels like a mini celebration—you’ll understand once you try them!

Seven small cheesecakes sit on a white, wavy-edged cake stand with a smooth, glossy surface. Each cheesecake is inside a white paper cup with a red grid pattern. The base layer is pale and creamy, topped with a shiny, deep red cherry topping filled with whole cherries and thick sauce that spills slightly over the edges. The background is a white marbled texture. 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 remember making these for a neighborhood potluck and how quickly they vanished—I think it’s because they look fancy but are so easy to whip up. This Cherry Cheesecake Cupcakes Recipe is all about delivering maximum flavor with minimum fuss. Plus, they’re perfectly bite-sized, making them ideal for sharing or sneaking a few whenever you want.

Simplicity Meets Elegance: You’ll create something impressive without needing a degree in baking.
Flavor Explosion: The smooth cream cheese combined with tart cherry pie filling makes every bite unforgettable.
Perfect Portions: Cupcake size means no cutting, no mess, and beautiful presentation every single time.
Flexible Timing: Bake one tray at a time at your own pace, so there’s no rush or stress.

The image shows many small cheesecakes arranged in rows on a black cooling rack, each in white paper cups with red patterns. Each cheesecake has two visible layers: a smooth, creamy white base and a glossy, bright red cherry topping with whole cherries and syrup that looks slightly shiny. The cheesecakes are evenly spaced and the background is a white marbled texture. photo taken with an iphone --ar 2:3 --v 7

Ingredients & Why They Work

Each ingredient in this Cherry Cheesecake Cupcakes Recipe plays a special role that builds up layers of flavor and texture. The vanilla wafers form a crunchy base that contrasts beautifully with the luscious cream cheese filling. And the lemon juice? It brightens things up, cutting through the richness just right.

Flat lay of a small stack of round vanilla wafers with a golden-brown color, three blocks of smooth cream cheese with creamy white texture, a small white bowl filled with fine granulated sugar, four whole clean eggs with light brown shells, a few fresh lemons cut in half with bright yellow flesh, and a small white bowl heaped with glossy deep red cherry pie filling, all arranged symmetrically on simple white ceramic dishes 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 act as your cupcake crust—light, sweet, and perfectly crisp.
Cream cheese: The star of the show, make sure it’s softened to room temperature for smooth mixing.
Sugar: Sweetens the filling just enough without being overpowering.
Eggs: They provide structure, so the cupcakes hold their shape without being dense.
Fresh lemon juice: Adds brightness and prevents the richness from feeling too heavy.
Cherry pie filling: The crowning jewel that adds vivid color and a fruity punch.

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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

What I love about this recipe is how easy it is to personalize. Sometimes I swap the vanilla wafers for gluten-free cookie options or top the cherry filling with a sprinkle of chopped toasted almonds for a textural contrast. You can really make it your own without losing the essence of those creamy, dreamy cheesecake cupcakes.

Variation: I once experimented by folding in a handful of mini chocolate chips right into the cream cheese batter—delicious! It gives these cupcakes a subtle chocolate surprise without overwhelming the cherry flavor.

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

Step 1: Prep with Cake Boss Care

First things first, preheat your oven to 350°F (175°C). This preheating step is crucial for even baking. While the oven warms, make sure your cream cheese is soft—it mixes so much better and prevents lumps in your batter.

Step 2: Creamy Batter Magic

Grab your mixer and blend together cream cheese, sugar, eggs, and fresh lemon juice until you have a perfectly smooth, creamy batter. I like to scrape down the sides of the bowl a couple of times to make sure everything incorporates evenly.

Step 3: Build Your Cupcakes

Line your muffin tin with paper liners—it makes cleanup a breeze and helps your cupcakes pop out easily. Place one vanilla wafer at the bottom of each cup as your base. Then, carefully spoon the cream cheese batter over the wafers, filling each cup about three-quarters full to give them space to rise.

Step 4: Bake with Patience

This recipe makes about 30 cupcakes, but here’s a pro tip: bake them one tray at a time to ensure they bake evenly and have that perfect texture. Bake each tray for about 20 to 22 minutes. You’ll notice the centers might sink a bit as they cool—that's totally normal, so don’t worry!

Step 5: The Cherry Finale

Once completely cooled, scoop a nice spoonful of cherry pie filling right into the center of each cupcake. Refrigerate for at least one hour—this chilling step helps the flavors meld and makes them extra refreshing.

Top Tip

Over the years, I’ve learned a few tricks that really make this Cherry Cheesecake Cupcakes Recipe shine—simple adjustments that prevent common pitfalls and keep your cupcakes looking and tasting fantastic.

Room Temperature Ingredients: Make sure your cream cheese and eggs are at room temp. Cold ingredients can lead to a lumpy batter and uneven baking.
Bake One Tray at a Time: This avoids uneven heat exposure and ensures every cupcake is perfectly baked through.
Don’t Panic About Sinking Centers: That sinking is expected—it’s a sign that the cheesecake centers are creamy and moist, not undercooked.
Chill Before Serving: Give them at least an hour in the fridge to set properly and bring out the flavors.

How to Serve Cherry Cheesecake Cupcakes Recipe

cherry cheesecake cupcakes - Serving Suggestion

Garnishes

I like to keep it classic with just the cherry pie filling on top, but for a special touch, a little dollop of whipped cream sprinkled with chopped pistachios or a light dusting of powdered sugar can elevate these cupcakes beautifully. Fresh cherries or mint leaves make for a pretty garnish if you’re serving for guests.

Side Dishes

These cupcakes pair wonderfully with a cup of black coffee or a light herbal tea—something that balances their sweet richness without overpowering it. For brunch, I’ve served them alongside fresh fruit salad and yogurt, which makes for a balanced, indulgent spread.

Creative Ways to Present

One of my favorite ways to make these cupcakes feel festive is to arrange them on a tiered dessert stand—sprinkle edible rose petals or colorful sugar crystals around for an elegant vibe. They also make adorable favors if wrapped in cellophane with a ribbon for holidays or parties.

Make Ahead and Storage

Storing Leftovers

I always keep leftovers in an airtight container in the fridge. They hold up beautifully for 3 to 4 days—just make sure you refrigerate them promptly to maintain that creamy texture and fresh cherry topping.

Freezing

If you want to freeze these cupcakes, I recommend freezing them before adding the cherry topping. Wrap each cupcake tightly in plastic wrap, then place them in a freezer bag. Thaw overnight in the fridge and add fresh cherry filling before serving for best results.

Reheating

Typically, I enjoy these chilled, but if you want to warm one slightly, I gently microwave it for about 10 seconds—just enough to take the chill off but not so much that the cheesecake texture breaks down.

Frequently Asked Questions:

Can I use frozen cherries instead of cherry pie filling?

While frozen cherries can work, cherry pie filling is thicker and sweeter, acting as a perfect topping that stays in place. If you use frozen cherries, consider cooking them down with sugar to mimic the pie filling’s texture and sweetness.

Why do the centers of my cupcakes sink?

The sinking centers are common with cheesecake cupcakes due to the batter’s density and moisture content. It means they’re moist and creamy inside—just let them cool completely to set properly, and don’t worry, it won’t affect the taste or texture negatively.

Can I make these cupcakes vegan or dairy-free?

Making these vegan or dairy-free is a bit tricky because cream cheese is central to the flavor and texture. However, you can experiment with dairy-free cream cheese alternatives and egg substitutes, but results may vary in texture and baking time.

Can I prepare the batter ahead of time?

You can prepare the batter a few hours in advance and keep it covered in the fridge. Bring it back to room temperature and give it a quick stir before filling the cups to ensure the best texture and even baking.

Final Thoughts

I genuinely adore how this Cherry Cheesecake Cupcakes Recipe combines ease and elegance. Whenever I pull out these cupcakes, they spark joy; it’s like sharing a little homemade love wrapped in each bite. You’ll find yourself reaching for one more before you know it—so go ahead, bake a batch, and watch them disappear with smiles all around.