Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting Recipe
If you love bright, fresh flavors with a little surprise inside, these Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting are bound to make your dessert dreams come true. Each bite delivers soft and fluffy lemon cake, a silky cheesecake filling at the heart, and a swirl of creamy lemon frosting on top – all working together in one seriously irresistible treat. With just the right zing and sweetness, these cupcakes are perfect for impressing family, friends, or even just treating yourself to a sunny pick-me-up.

Ingredients You’ll Need
It all starts with a few simple but essential ingredients you probably already have on hand. Each plays a special part in bringing the Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting to life, creating a treat that’s equal parts moist, tangy, and creamy.
- All-purpose flour: Gives the cupcakes a light but sturdy structure that holds up to the creamy filling.
- Baking powder & baking soda: These are the secret to fluffy cupcakes with the perfect rise.
- Salt: Just a pinch enhances all the vibrant flavors.
- Unsalted butter (softened): Brings that melt-in-your-mouth richness to both cupcakes and frosting.
- Granulated sugar: Sweetens both the cupcakes and the luscious cheesecake surprise inside.
- Large eggs: Help the batter emulsify, giving your cupcakes a tender crumb.
- Sour cream: Adds moisture and a hint of tang for that classic bakery texture.
- Whole milk: Ensures the cupcakes are soft, not dense.
- Lemon juice & lemon zest: These deliver the bold citrus flavor and sunny color you crave.
- Vanilla extract: Rounds out the flavors with a bit of warmth and sweetness.
- Cream cheese (softened): The star of the rich cheesecake filling nestled inside each cupcake.
- Powdered sugar: Sweetens and thickens your lemony frosting for smooth, fluffy swirls.
- Heavy cream or milk: Helps you achieve the perfect creamy frosting consistency.
- Pinch of salt (for frosting): Balances and sharpens the sweet and citrus notes.
How to Make Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting
Step 1: Prepare Your Cupcake Pan and Preheat the Oven
Begin by heating your oven to 350°F (175°C). Line a 12-cup muffin pan with your favorite cupcake liners. This small step ensures your Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting bake evenly and are easy to remove after baking.
Step 2: Mix the Dry Ingredients
In a medium bowl, whisk the flour, baking powder, baking soda, and salt. This ensures all the leaveners are evenly distributed, setting your cupcakes up for the perfect rise and texture.
Step 3: Cream the Butter and Sugar
In a large mixing bowl, beat the softened butter and granulated sugar together until the mixture is light and fluffy. This step creates air bubbles that make the cupcakes delightfully tender.
Step 4: Incorporate Eggs and Wet Ingredients
Add the eggs one at a time, beating well after each addition. Next, mix in the sour cream, whole milk, lemon juice, lemon zest, and vanilla extract. The hint of sour cream and that burst of citrus really shine in this unique cupcake base.
Step 5: Combine Dry and Wet Mixtures
Gradually add the whisked dry ingredients to the wet batter, mixing until just combined. Over-mixing can make your cupcakes tough, so stop as soon as you no longer see streaks of flour.
Step 6: Make the Cheesecake Filling
In a small bowl, beat the softened cream cheese, sugar, and vanilla extract until perfectly smooth. This creamy filling is what makes these Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting truly special!
Step 7: Fill the Cupcake Liners
Spoon about one-third full of lemon batter into each lined cupcake slot. Add a heaping teaspoon of the cheesecake filling in the center of each, then cover with more cupcake batter until the liners are about three-quarters full. This ensures every cupcake gets its hidden cheesecake heart.
Step 8: Bake
Bake the cupcakes for 18 to 20 minutes, or until the tops spring back when touched and a toothpick inserted just off-center comes out clean (avoiding the cheesecake center). Let the cupcakes cool completely before frosting—patience pays off here!
Step 9: Make the Lemon Frosting
Beat the softened butter until creamy and smooth. Now, gradually add powdered sugar, lemon juice, lemon zest, and a pinch of salt. Whip until fluffy, then add heavy cream or milk as needed to get your desired consistency. The result is a tangy, bright lemon frosting that’s simply heavenly on these Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting.
Step 10: Frost and Decorate
Once your cupcakes are fully cooled, pipe or spread the frosting generously on top. For that extra pop, garnish with more lemon zest or a thin lemon slice. The finishing touch makes these cupcakes truly irresistible!
How to Serve Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting

Garnishes
A classic touch is a sprinkle of fresh lemon zest over the tops, which not only looks beautiful but adds a punch of citrus fragrance. For a more sophisticated look, a thin lemon slice, a twist of lemon peel, or even a few edible flowers works wonders. These small details really set your Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting apart at any gathering.
Side Dishes
If you’re serving these cupcakes as part of a dessert spread, pair them with fresh berries, a simple fruit salad, or a scoop of fruity sorbet. Light, crisp sides help balance out the creamy, rich decadence of Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting and keep things feeling fresh.
Creative Ways to Present
For an unforgettable display, arrange the cupcakes on a pretty cake stand and scatter lemon slices and mint leaves around. For parties, place each cupcake in a decorative wrapper or clear box for a picnic-perfect treat. Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting can also be topped with a dusting of powdered sugar or edible glitter for a bit of extra sparkle.
Make Ahead and Storage
Storing Leftovers
These cupcakes keep best in an airtight container in the refrigerator, where they’ll stay fresh for up to 4 days. Because of the cheesecake filling and tangy frosting, it’s important to keep Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting chilled—just let them come to room temperature before serving for the softest texture and fullest flavor.
Freezing
If you want to save some cupcakes for later, freeze them unfrosted by wrapping each tightly in plastic and storing in a freezer-safe bag or container. Thaw overnight in the fridge, then add the fresh lemon frosting before serving for that just-baked taste.
Reheating
While you won’t need to reheat these cupcakes, if you’ve pulled them straight from the fridge, letting them sit at room temperature for 30–40 minutes will bring back their soft, luscious texture. Frosting can be whipped again if it starts to stiffen during storage.
FAQs
Can I use bottled lemon juice instead of fresh?
You can use bottled lemon juice in a pinch, but fresh lemon juice and zest will give your Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting the brightest, truest citrus flavor and aroma.
Can I make these cupcakes gluten-free?
Yes, substitute your favorite gluten-free all-purpose flour blend for the standard flour. Make sure it contains xanthan gum for the best cupcake texture.
Why is my cheesecake filling sinking?
If your filling sinks, it’s likely the batter was too thin or the filling was too heavy. Make sure to use softened (not melted) cream cheese, and don’t overfill the cupcakes with either batter or filling.
Can I make the cupcakes a day ahead?
Absolutely! In fact, making them a day before gives the flavors a chance to meld. Just store the frosted Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting in the fridge, and let them warm up a bit before serving.
How can I get extra lemon flavor?
Mix in a few drops of pure lemon extract to the cupcake batter or frosting, or add extra freshly grated zest for a bigger citrus punch!
Final Thoughts
Bringing together the lightness of lemon cake, the indulgence of cheesecake, and the zing of lemon frosting, these Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting are a delightful treat you’ll want to make again and again. Whether for a special occasion or simply to brighten a cloudy day, I hope you’ll love every bite. Go ahead, give these a try—you deserve a little cupcake magic!
Print
Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting Recipe
- Total Time: 45 minutes
- Yield: 12 cupcakes 1x
- Diet: Vegetarian
Description
Indulge in the delightful combination of creamy cheesecake filling stuffed inside zesty lemon cupcakes, topped with a luscious lemon frosting. These Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting are a perfect treat for any occasion!
Ingredients
For the Cupcakes:
- 1½ cups all-purpose flour
- 1 teaspoon baking powder
- ¼ teaspoon baking soda
- ¼ teaspoon salt
- ½ cup unsalted butter, softened
- ¾ cup granulated sugar
- 2 large eggs
- ¼ cup sour cream
- ¼ cup whole milk
- 2 tablespoons lemon juice
- 1 tablespoon lemon zest
- 1 teaspoon vanilla extract
For the Cheesecake Filling:
- 8 oz cream cheese, softened
- ¼ cup granulated sugar
- 1 teaspoon vanilla extract
For the Lemon Frosting:
- 1 cup unsalted butter, softened
- 3½ cups powdered sugar
- 2 tablespoons lemon juice
- 1 tablespoon lemon zest
- 1–2 tablespoons heavy cream or milk
- pinch of salt
Instructions
- Preheat the oven: Preheat the oven to 350°F (175°C) and line a 12-cup muffin pan with cupcake liners.
- Mix dry ingredients: Whisk together flour, baking powder, baking soda, and salt in a medium bowl.
- Cream butter and sugar: In a large bowl, cream butter and sugar until light and fluffy.
- Add wet ingredients: Beat in eggs, then add sour cream, milk, lemon juice, lemon zest, and vanilla extract. Mix until smooth.
- Prepare cheesecake filling: Beat cream cheese, sugar, and vanilla until smooth.
- Fill cupcake liners: Fill liners with lemon batter, add cheesecake filling, then top with more batter. Bake until done.
- Make frosting: Beat butter, powdered sugar, lemon juice, lemon zest, and salt until fluffy. Add cream as needed for consistency.
- Frost cupcakes: Pipe or spread frosting on cooled cupcakes. Garnish with lemon zest or slices.
Notes
- Ensure cupcakes are fully cooled before frosting.
- For a stronger lemon flavor, use lemon extract.
- Store cupcakes in the fridge and bring to room temperature before serving.
- Prep Time: 25 minutes
- Cook Time: 20 minutes
- Category: Dessert
- Method: Baking
- Cuisine: American
Nutrition
- Serving Size: 1 cupcake
- Calories: 360
- Sugar: 32g
- Sodium: 140mg
- Fat: 20g
- Saturated Fat: 12g
- Unsaturated Fat: 7g
- Trans Fat: 0g
- Carbohydrates: 42g
- Fiber: 0g
- Protein: 4g
- Cholesterol: 70mg