This post may contain affiliate links.
Lemon Cheesecake Cupcakes are bright, tangy lemon cupcakes with a creamy cheesecake pudding center and a swirl of lemon cream cheese frosting. I bake these whenever we need a sunshine-in-a-bite treat, and the girls love discovering the surprise filling tucked inside. They are bursting with fresh lemon flavor, just like our lemon cake.
These lemon cheesecake cupcakes are a fun, filled twist on a classic lemon cupcake.
Lemon Cheesecake Cupcakes Quick Look
- 🕒 Prep Time: 20 minutes
- 🌡️ Cook Time: 25 minutes
- ⏳ Total Time: 45 minutes
- 🍽️ Serving: 24 servings
- ⚡ Calories: 307kcal
- 🌶️ Flavor Profile: Bright, tangy lemon cake with a creamy cheesecake center and lemon frosting
- ✋ Difficulty: Easy, a fun filled cupcake
Quick Answer
To make Lemon Cheesecake Cupcakes, bake bright lemon cupcakes, then make a lemon cream cheese frosting and a quick cheesecake pudding filling. Scoop a center out of each cooled cupcake, fill it with the cheesecake pudding, and pipe the lemon frosting on top. Finish each with a little lemon wedge.
Jump to:
- Lemon Cheesecake Cupcakes Quick Look
- Quick Answer
- Why This Recipe Works
- Why You’ll Love This Recipe
- Key Ingredients
- Variations and Substitutions
- How to Make Lemon Cheesecake Cupcakes
- Recipe Tips & Tricks
- Serving Ideas and Suggestions
- Lemon Cheesecake Cupcakes FAQs
- Other Recommended Lemon Dessert Recipes
- Lemon Cheesecake Cupcakes
Why This Recipe Works
Click to see the technique science
- Fresh lemon juice and zest do the heavy lifting. Using both the juice and the zest gives the cupcakes a bright, real lemon flavor, not an artificial one.
- The cheesecake pudding center is a fun surprise. A quick cheesecake pudding filling tucked inside makes every bite creamy and adds a tangy cheesecake note.
- Cream cheese frosting balances the sweetness. Whipping cream cheese into the frosting keeps it from being too sweet and echoes the cheesecake filling.
- Filling the liners halfway gives the perfect dome. Not overfilling lets the cupcakes rise into a tidy dome that is easy to fill and frost.
- A toothpick test guarantees moist cupcakes. Pulling them the moment a toothpick comes out clean keeps the lemon cupcakes soft and moist.
Why You’ll Love This Recipe
- Every bite has a tangy lemon cupcake, a creamy cheesecake center, and lemon frosting.
- They look bakery-pretty but are easy enough for a weekend bake with the kids.
- They are perfect for spring, Easter, and summer parties alongside our pina colada cupcakes.
Key Ingredients
Here is what you need for these bright Lemon Cheesecake Cupcakes.
- Fresh Lemons: Both the juice and the zest give the cupcakes and frosting real, vibrant lemon flavor.
- Cheesecake Pudding Mix: Whisked with milk, it makes the creamy cheesecake center hidden inside each cupcake.
- Cream Cheese: Whipped into the frosting for a tangy, not-too-sweet lemon cream cheese topping.
- Butter, Sugar, and Eggs: The base of a classic, tender lemon cupcake.
- Flour, Baking Powder, and Milk: Build the soft, fluffy cupcake crumb.
See recipe card for exact quantities.
Variations and Substitutions
These Lemon Cheesecake Cupcakes are easy to make your own.
- Add blueberries: Fold fresh blueberries into the batter for lemon-blueberry cupcakes.
- Use lemon curd: Fill the centers with lemon curd instead of cheesecake pudding for an extra tart surprise.
- Make them mini: Bake in a mini muffin pan and reduce the time for bite-sized treats.
- Switch the citrus: Use lime or orange juice and zest for a different citrus cupcake.
- Skip the color: Leave out the food coloring for a natural, pale lemon frosting.
How to Make Lemon Cheesecake Cupcakes
- Make the lemon batter. Cream the butter, sugar, and vanilla, beat in the eggs, then mix in the lemon juice and zest, followed by the flour, baking powder, salt, and milk.
- Make the frosting. Whip the softened butter and cream cheese, gradually beat in the powdered sugar, then fold in lemon juice, zest, and a few drops of yellow food coloring.
- Fill the liners. Stir the batter until smooth, then fill the paper-lined muffin cups halfway full.
- Bake the cupcakes. Bake at 350 degrees for 20 to 25 minutes, until a toothpick comes out clean, then cool completely.
- Fill with cheesecake pudding. Whisk the cheesecake pudding mix with milk, scoop a small center out of each cooled cupcake, and fill it with a spoonful of pudding.
- Frost the cupcakes. Pipe the lemon frosting onto each cupcake in a swirl with a star tip and top with a lemon wedge.
Recipe Tips & Tricks
- Zest before you juice, it is much easier to zest a whole lemon than a squeezed one.
- Use room-temperature butter, cream cheese, and eggs so everything creams together smoothly.
- Do not overfill the liners, halfway gives the best dome and room for filling.
- Cool completely before filling, warm cupcakes will melt the pudding center and frosting.
- Chill the frosting for a few minutes if it gets soft so it pipes into clean swirls.
- Add the lemon wedge garnish just before serving so it stays fresh and pretty.
Serving Ideas and Suggestions
Serve these Lemon Cheesecake Cupcakes chilled or at room temperature, each one topped with a swirl of lemon frosting and a little lemon wedge. They are a bright, cheerful addition to any spring or summer dessert table.
They pair beautifully with other citrus desserts. Set them out next to our meltaway lemon cookies and a lemon blueberry poke cake for a lemon-lovers spread.
Hosting a party or shower? Make these cupcakes ahead, keep them chilled, and frost them the day of. They are lovely alongside our pina colada cupcakes for a fun cupcake bar.
Lemon Cheesecake Cupcakes FAQs
The filling in Lemon Cheesecake Cupcakes is a quick cheesecake pudding made by whisking instant cheesecake pudding mix with milk. It is spooned into the center of each cooled cupcake for a creamy, tangy surprise.
Yes, bake the Lemon Cheesecake Cupcakes a day ahead and store them airtight. Fill and frost them the day you plan to serve, then keep them chilled until ready.
Because of the cream cheese frosting and pudding filling, store Lemon Cheesecake Cupcakes in an airtight container in the refrigerator for up to 3 days. Let them sit out a few minutes before serving.
Yes, you can shortcut Lemon Cheesecake Cupcakes by baking a lemon boxed cake mix into cupcakes, then adding the cheesecake pudding filling and homemade lemon cream cheese frosting.
Cupcakes can sink if the batter is overmixed or the oven door is opened too early. Mix the Lemon Cheesecake Cupcakes batter just until combined and keep the oven closed until they are nearly done.
Use a small spoon to scoop a center out of each cooled cupcake, going about halfway down without piercing the bottom, then fill it with cheesecake pudding. The frosting on top hides the opening.
Love all things lemon? Try our melt-in-your-mouth meltaway lemon cookies next.
Looking for a cute cupcake? Try our Dirt Cupcakes baked in terracotta pots.
Love a citrus cupcake? Our lemon cupcakes are bright and tangy with a sweet strawberry buttercream swirl.
More lemon goodness ahead, our lemon brownies are easy, fudgy, and one bowl.
Lemon Cheesecake Cupcakes
Ingredients
- 2 & 1/4 cups all-purpose flour
- 1 & 2/3 cups granulated sugar
- 2/3 cup unsalted butter
- 1 & 1/4 cups milk
- 4 teaspoons baking powder
- 1 teaspoon salt
- 1 teaspoon vanilla extract
- 3 large eggs
- 1 teaspoon lemon zest
- 1/4 cup lemon Juice fresh squeezed
For the filling:
- 3.3 ounce box instant cheesecake pudding
- 1 & 1/2 cups milk
For the frosting:
- 1/2 cup butter softened
- 4 ounces cream cheese softened
- 16 ounces powdered sugar sifted
- 1 tablespoon Lemon juice fresh squeezed
- 1 teaspoon lemon zest
- Yellow gel food coloring
Instructions
- Heat the oven to 350°F. Fill 24 muffin cups with paper liners and set aside.
- In a large bowl, cream the butter, sugar, and vanilla until light and fluffy for about 1 minute, scraping the side of the bowl to make sure all ingredients are mixed well.
- Add the eggs and mix well until the egg and sugar mixture is light and fluffy.
- Next, add lemon juice and lemon zest, stir until fully combined.
- Add the flour, baking powder, and salt to the lemon cupcake batter and stir until combined. While stirring, add the milk until everything is fully combined and the cake batter has formed.
- Fill paper-lined muffin cups 1/2 full.
- Bake for 20-25 minutes, or until a toothpick inserted into the center comes out clean. Let cool in the tin for 5 minutes, then place on a wire rack to cool completely.
- In a large bowl, whip the softened butter and cream cheese until creamy.
- Gradually add the powdered sugar, one cup at a time, beating well after each addition.
- Finally, fold in the lemon juice and zest, then add a few drops of yellow food coloring gel, until well incorporated. Set aside.
- Make the cheesecake pudding by whisking together the cheesecake pudding mix and milk for 2 minutes, and set aside.
- Using a small spoon, insert it into the center of the cupcake, going about halfway down. Twist the spoon slightly if needed. Be careful not to pierce the bottom. Fill the cupcake with a spoonful of cheesecake pudding.
- Add frosting to a piping bag with a star tip and pipe frosting on each cupcake in a swirl pattern, then top with a lemon wedge, if using.
Nutrition
Love This Recipe?
Follow @ThisSillyGirlsKitchen on Instagram and @danadevolk on Pinterest for more!
