Few desserts capture the essence of fresh, sunny flavors quite like Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting. Each bite delivers a bright burst of lemony cake cloaking a secret pocket of rich, creamy cheesecake, all crowned with a cloud of luscious lemon frosting. Whether you’re baking to celebrate spring, impress family at brunch, or just to brighten your own afternoon, this recipe promises tangy, decadent joy in every cupcake.

Ingredients You’ll Need
These Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting come together with pantry staples and a dose of citrus magic. Every ingredient plays its part — from the sunny lemon zest to the dreamy cream cheese — creating cupcakes that are soft, creamy, and utterly irresistible.
- All-purpose flour: The sturdy base that gives the cupcakes their perfect crumb and soft bite.
- Baking powder and baking soda: Team up for light, airy cupcakes that rise tall, tender, and fluffy.
- Salt: Just a pinch balances all the sweetness and sharpens the lemony zing.
- Unsalted butter (softened): Brings richness and moisture, ensuring the batter is smooth and the frosting creamy.
- Granulated sugar: Adds sweetness and helps the cupcakes and cheesecake filling bake up golden.
- Large eggs: Bind everything together and add structure for that perfect cupcake dome.
- Lemon zest: Packs natural oils and pure citrus fragrance for maximum lemon flavor.
- Fresh lemon juice: Offers tart freshness that wakes up every bite (avoid bottled for the best flavor!).
- Vanilla extract: Adds warmth and rounds out the citrus punch in both the cake and the filling.
- Sour cream: Infuses moisture and a gentle tang, keeping the crumb rich but not heavy.
- Milk: Loosens the batter to just the right consistency for tender cupcakes.
- Cream cheese (softened): Makes the secret filling decadently creamy, contrasting beautifully with zippy lemon.
- Powdered sugar: Gives the frosting body and a silky texture that’s sweet but not gritty.
- Heavy cream: Fluffs up the frosting, making it cloud-like and perfect for piping or spreading.
- Pinch of salt: A small but mighty ingredient — it makes all the sweet and tart notes sing in harmony.
How to Make Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting
Step 1: Prep Your Oven and Pan
Begin by preheating your oven to 350°F (175°C). Line a 12-cup muffin pan with paper liners; this not only ensures an easy release but adds a festive touch to your finished cupcakes. A little preparation now means perfectly baked treats later!
Step 2: Mix the Dry Ingredients
In a medium bowl, whisk together the flour, baking powder, baking soda, and salt. This step evenly distributes the leaveners and salt throughout the flour to guarantee uniformly risen, tender cupcakes.
Step 3: Cream the Butter and Sugar
In a large mixing bowl, beat the softened butter and granulated sugar until the mixture is light and fluffy. This step is where air gets incorporated, promising cupcakes with lift and a wonderfully delicate texture.
Step 4: Add the Wet Ingredients
Beat in the eggs, one at a time, mixing well after each addition. Next, stir in the lemon zest, lemon juice, and vanilla extract, infusing the batter with those signature zesty notes. Gently add the sour cream and milk, blending just until smooth and creamy.
Step 5: Combine Wet and Dry Mixtures
Gradually add the dry ingredients from Step 2 to your wet mixture, mixing only until just incorporated. Overmixing can make the cupcakes tough, so stop as soon as you see no dry streaks.
Step 6: Make the Cheesecake Filling
In a small bowl, beat together the cream cheese, sugar, and vanilla extract until the filling is completely smooth and thick. This luscious layer will melt into the center of the cupcakes, creating a delightful surprise with every bite.
Step 7: Assemble the Cupcakes
Spoon about one third of the lemon batter into each cupcake liner. Drop a heaping teaspoon of the cream cheese mixture into the center of each, then cover with more lemon batter until just about two thirds full. This layering gives you that perfect cheesecake core!
Step 8: Bake and Cool
Bake in the preheated oven for 18–22 minutes, or until the tops spring back gently when touched and a toothpick inserted into the cupcake edge (not the center cheesecake) comes out clean. Allow cupcakes to cool in the pan for a few minutes, then transfer them to a wire rack to cool completely before frosting.
Step 9: Make the Lemon Frosting
Beat the softened butter until creamy, then gradually mix in powdered sugar, alternating with lemon juice and zest. Add heavy cream and a pinch of salt, whisking until the frosting is fluffy and light. Beat on high for a couple of minutes for that bakery-style finish.
Step 10: Frost and Decorate
Once the cupcakes are completely cool, frost generously with your lemon frosting. A simple swirl, rosette, or a mound — whichever way you go, finish with extra lemon zest or thin lemon slices for a beautiful, zesty flourish!
How to Serve Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting

Garnishes
A simple scattering of fresh lemon zest over the frosting breathes extra sparkle to each cupcake. For a showstopper effect, perch a thin slice of lemon or a pretty edible flower on top — the colors and shapes make every Cheesecake Stuffed Lemon Cupcake with Lemon Frosting impossible to resist!
Side Dishes
Pair these tangy treats with fresh berries — raspberries, blueberries, or strawberries complement the lemon and cheesecake beautifully. A pitcher of iced tea or lemonade on the side turns your cupcakes into a centerpiece for any afternoon tea or garden party.
Creative Ways to Present
Try presenting your Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting in colorful cupcake wrappers or stacked on a tiered stand for a charming dessert table display. For a playful twist, serve them in individual mason jars with a tiny fork tucked in, making them perfect for picnics or party favors.
Make Ahead and Storage
Storing Leftovers
Keep any leftover cupcakes in an airtight container in the refrigerator for up to four days. Thanks to the creamy cheesecake center and the fresh lemon frosting, Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting stay moist and delicious even after chilling — just be sure to bring them to room temperature before serving for the dreamiest texture.
Freezing
These cupcakes freeze surprisingly well! Freeze unfrosted cupcakes and cheesecake centers together, then wrap tightly and store for up to two months. Simply thaw the cupcakes overnight in the fridge and frost them fresh for best flavor and texture.
Reheating
While Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting are meant to be enjoyed at room temperature or lightly chilled, you can revive any slightly dry cupcakes by microwaving them (without frosting) for 8-10 seconds. Always add frosting after reheating for the best experience.
FAQs
Can I use bottled lemon juice?
Fresh lemon juice is highly recommended for the boldest citrus flavor. Bottled juice can taste muted and sometimes even harsh, so if possible, always reach for fresh lemons when making Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting.
Can I double the recipe?
Absolutely! This recipe doubles beautifully, so you can easily make 24 cupcakes if you’re serving a crowd. Just be sure to bake in batches for even results.
How do I know when the cupcakes are perfectly baked?
Check for springy tops and a toothpick test near the edge of the cupcake (not the cheesecake center). You want the cakes to be golden and set, with no wet batter sticking to the sides.
Can I make these gluten-free?
Yes, a good 1:1 gluten-free all-purpose flour substitute will yield cupcakes that are just as moist and flavorful. Be sure to check that your baking powder and other ingredients are gluten-free as well.
Why is my cheesecake filling runny?
This usually occurs if the cream cheese was too soft or if you accidentally overbeat it. For the perfect core, use room temperature but not melting cream cheese, and beat just until smooth and thick.
Final Thoughts
There’s nothing quite as cheerful as a platter of Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting. Each one is a sunshiny surprise wrapped up in sweet, creamy, citrusy layers. Give this recipe a try — you’ll want to bake them again and again for every special moment that deserves a little extra zest!
Print
Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting Recipe
- Prep Time: 25 minutes
- Cook Time: 20 minutes
- Total Time: 45 minutes
- Yield: 12 cupcakes
- Category: Dessert
- Method: Baking
- Cuisine: American
- Diet: Vegetarian
Description
Indulge in these delightful Cheesecake Stuffed Lemon Cupcakes with a zesty Lemon Frosting. A perfect combination of tangy lemon and creamy cheesecake in a moist cupcake.
Ingredients
For the cupcakes:
- 1 ½ cups all-purpose flour
- 1 ½ teaspoons baking powder
- ¼ teaspoon baking soda
- ¼ teaspoon salt
- ½ cup unsalted butter (softened)
- 1 cup granulated sugar
- 2 large eggs
- 1 tablespoon lemon zest
- 2 tablespoons fresh lemon juice
- ½ teaspoon vanilla extract
- ½ cup sour cream
- ¼ cup milk
For the cheesecake filling:
- 6 ounces cream cheese (softened)
- ¼ cup granulated sugar
- 1 teaspoon vanilla extract
For the lemon frosting:
- ½ cup unsalted butter (softened)
- 4 cups powdered sugar
- 2–3 tablespoons fresh lemon juice
- 1 teaspoon lemon zest
- 2 tablespoons heavy cream (or as needed)
- pinch of salt
Instructions
- Preheat the oven and prepare the pan: Preheat oven to 350°F (175°C) and line a 12-cup muffin pan with paper liners.
- Prepare the cupcake batter: Mix dry ingredients, beat butter and sugar, add eggs and flavorings, alternate with dry ingredients, and mix until combined.
- Make the cheesecake filling: Beat cream cheese, sugar, and vanilla until smooth.
- Fill the cupcake liners: Layer batter and cheesecake mixture in the liners.
- Bake the cupcakes: Bake for 18–22 minutes until done, then cool on a wire rack.
- Prepare the lemon frosting: Beat butter, add powdered sugar, lemon juice, zest, salt, and cream to desired consistency.
- Frost the cupcakes: Frost cooled cupcakes and garnish with lemon zest or slices.
Notes
- Ensure the cheesecake filling is thick for better results.
- Substitute lemon extract for a stronger flavor.
- Store cupcakes in the fridge for up to 4 days.
Nutrition
- Serving Size: 1 cupcake
- Calories: 420
- Sugar: 38g
- Sodium: 210mg
- Fat: 22g
- Saturated Fat: 13g
- Unsaturated Fat: 8g
- Trans Fat: 0g
- Carbohydrates: 53g
- Fiber: 1g
- Protein: 4g
- Cholesterol: 75mg