Cherry Cheesecake Cupcakes Bites

Category: Treats That Make Everything Better

Enjoy delightful cherry cheesecake cupcakes with a crisp vanilla wafer base and a smooth, creamy filling. Made in a muffin pan, these treats combine softened cream cheese, eggs, sugar, lemon juice, and vanilla, then are finished with a sweet cherry topping. Simple to prepare and serve, they cool quickly and are perfect for sharing at parties or family get-togethers. Their individual portions offer a light, luscious bite, balancing tangy cheesecake flavor with the fruity brightness of cherries and the subtle crunch of the wafer.

Lili Clark smiling at the camera.
Created By Lili Clark
Updated on Thu, 27 Nov 2025 17:15:50 GMT
A person holding a cupcake with cherries and cream. Save
A person holding a cupcake with cherries and cream. | lilicooks.com

Cherry Cheesecake Cupcakes are the dreamy dessert I turn to when I want something quick but still showstopping. These single-serve treats give you all that classic creamy cheesecake flavor on a vanilla wafer base and are the hit of every party or family gathering.

I made these for my daughter’s birthday picnic and they disappeared before the sandwiches. Now we make them every spring because everyone requests them for get-togethers and birthday treats.

Ingredients

  • Cupcake liners: keep everything clean and make the cheesecakes so easy to serve Try for unbleached liners for the best look
  • Vanilla wafers: form that perfect crunchy base Use a crisp fresh wafer for structure
  • Cream cheese: is the heart of the cheesecake Make sure it is fully softened for the smoothest batter Philadelphia brand or your favorite full-fat kind work best
  • Eggs: create a custard texture Choose fresh eggs with bright yolks for best color and flavor
  • Sugar: adds sweetness and helps with structure Look for fine granulated sugar for even blending
  • Lemon juice: gives a hit of brightness that lifts the whole flavor Freshly squeezed is worth the extra minute for a cleaner taste
  • Vanilla extract: gives that classic comforting aroma and warmth Pure vanilla makes a noticeable difference here
  • Cherry pie filling: is the sweet-tart finishing touch Use a high-quality pie filling with whole cherries for the prettiest cupcakes

Step-by-Step Instructions

Line the Pan:
Set paper cupcake liners in your muffin tin and place a vanilla wafer flat side down in each liner This forms your crust and keeps the cheesecake from sticking
Prepare the Cream Cheese Mixture:
In a medium bowl beat softened cream cheese with your mixer on medium speed Keep going until it is completely creamy with no lumps which ensures a velvety end result
Mix in Sugar Eggs and Flavor:
Add sugar eggs lemon juice and vanilla to the cream cheese Beat the mixture until everything is fluffy and smooth This step creates that signature cheesecake texture
Fill the Liners:
Spoon the cream cheese mixture into each liner filling about three quarters full This gives the perfect cupcake shape as they bake
Bake:
Place the pan on the center rack at 375 degrees Fahrenheit Bake for 15 to 20 minutes Check that the cheesecakes are just set but not browned The centers should jiggle slightly but not look wet
Cool Completely:
Let the cupcakes cool in the pan for a few minutes before moving to a wire rack to cool fully This prevents them from sinking
Top with Cherries:
Once the cheesecakes are completely cool spoon cherry pie filling onto the tops Use a heaping tablespoon per cupcake for that classic look
Cherry cheesecake cupcakes with a white cupcake wrapper. Save
Cherry cheesecake cupcakes with a white cupcake wrapper. | lilicooks.com

My favorite part is the burst of cherry with every bite It takes me right back to my grandmother’s kitchen where she would sneak me extra cherries for my slice I love watching my own kids sneak the same extra cherries every time we make these together

Storage Tips

Store any leftover cupcakes tightly covered in the refrigerator where they will keep for up to four days For longer storage you can freeze the cupcakes without topping for up to one month Once thawed add fresh pie filling just before serving This helps keep the crust crisp and the topping bright

Ingredient Substitutions

If you are out of vanilla wafers try graham crackers or digestive biscuits crushed and pressed into the liners You can swap in different fruit toppings like blueberry or strawberry pie filling or even homemade cooked fruit sauces For a citrusy twist replace the lemon juice with orange juice or zest

A cupcake with cherries on top. Save
A cupcake with cherries on top. | lilicooks.com

Serving Suggestions

Pile cupcakes on a pretty platter for a dessert buffet or pack them into lunchboxes for a sweet surprise They pair beautifully with a hot cup of coffee or tea and are just the right size for little hands Ice cream or freshly whipped cream on the side is always welcome if you want to go all out

Cultural Inspiration

Mini cheesecakes are an American classic and became popular thanks to the rise of home entertaining in the 1960s When I first baked these I was inspired by old-fashioned church potlucks and how little individual desserts make everyone feel special

Recipe FAQs

→ How do I prevent the cheesecake cups from cracking?

Be sure not to overmix the batter, and let the cupcakes cool gradually. Avoid opening the oven during baking.

→ Can I use a different fruit topping?

Absolutely! Try blueberry, strawberry, or even mixed berries for a different fruity twist.

→ Are vanilla wafers required for the base?

Vanilla wafers add a pleasant crunch, but you can substitute with graham cracker rounds or even cookies.

→ How should I store leftover cupcakes?

Refrigerate in an airtight container for up to 3-4 days to maintain freshness and texture.

→ Can these be made ahead of time?

Yes! Prepare and chill the cupcakes in advance, then top with cherries right before serving for best results.

→ Is a stand mixer necessary?

No, a hand mixer or sturdy whisk will work to blend the cream cheese mixture until smooth and fluffy.

Cherry Cheesecake Cupcakes Bites

Mini cheesecakes with cherry topping and vanilla wafer crust—perfect for sweet cravings and easy to share.

Preparation Time
15 min
Cooking Time
20 min
Overall Time
35 min
Created By: Lili Clark

Category: Desserts

Skill Level: Moderate

Cuisine Type: American

Output: 20 Serves (20 mini cheesecakes)

Dietary Options: Vegetarian

Ingredients

→ Base

01 20 cupcake liners
02 20 vanilla wafers

→ Filling

03 16 ounces cream cheese, softened
04 2 eggs
05 3/4 cup sugar
06 1 tablespoon lemon juice
07 1 teaspoon vanilla extract

→ Topping

08 21 ounces cherry pie filling

Steps

Step 01

Preheat oven to 375°F. Line a muffin pan with cupcake liners and place a vanilla wafer, flat side down, in the bottom of each liner.

Step 02

In a small bowl, beat the softened cream cheese. Add sugar, eggs, lemon juice, and vanilla extract; mix until fluffy and light.

Step 03

Fill each liner 3/4 full with the cream cheese mixture. Bake for 15 to 20 minutes or until set. Let cool completely before removing from the pan.

Step 04

Place mini cheesecakes on a serving tray. Top with cherry pie filling. Optionally, display additional toppings around the tray for customization.

Required Tools

  • Muffin pan
  • Silicone spatula
  • Stand mixer

Allergy Information

Always check each ingredient for allergens, and consult a medical professional if unsure.
  • Contains dairy (cream cheese)
  • Contains eggs

Nutritional Information (per serving)

These details are shared for general guidance and don’t replace professional advice.
  • Calories: 177
  • Fats: 9 g
  • Carbohydrates: 22 g
  • Proteins: 2 g