If you have a soft spot for bright, tangy sweets with a luscious surprise inside, then you will absolutely adore the Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting Recipe. Each cupcake bites into a tender, moist cake infused with fresh lemon zest and juice, only to reveal a creamy, dreamy cheesecake center that feels like a little celebration in every mouthful. Topped with a silky, zesty lemon frosting, these cupcakes balance the perfect amount of sweetness and tartness that will brighten any day or occasion. Whether you’re baking for a party, a special treat, or just because, this recipe brings an irresistible combination of flavors and textures that just can’t be beat.

Ingredients You’ll Need
These ingredients are delightfully simple yet essential, working together to create a harmonious blend of lemony freshness, creamy indulgence, and tender crumb. Every component plays a special role in making these cupcakes the irresistible treats they are.
- 1 ½ cups all-purpose flour: The foundation for soft, fluffy cupcakes with just the right texture.
- 1 ½ teaspoons baking powder: Helps the cupcakes rise beautifully to a light and airy height.
- ¼ teaspoon salt: Enhances all the flavors without overpowering the lemon zing.
- ½ cup unsalted butter, softened: Adds richness and moisture, making the cake tender and flavorful.
- 1 cup granulated sugar: Sweetens the cake perfectly while caramelizing slightly during baking for depth.
- 2 large eggs: Bind all the ingredients and provide structure for a light crumb.
- 1 teaspoon vanilla extract: Adds subtle warmth that balances the bright lemon.
- 2 tablespoons lemon zest: Packs incredible citrus punch, infusing the batter with fresh lemon oils.
- 2 tablespoons lemon juice: Brightens the flavor and moistens the batter naturally.
- ½ cup whole milk: Keeps the batter smooth and moist for tender crumb.
- 6 ounces cream cheese, softened: The star of the filling, adding creamy richness with a slight tang.
- 3 tablespoons granulated sugar (for filling): Sweetens the cheesecake center just right.
- 1 teaspoon vanilla extract (for filling): Enhances the smooth cream cheese flavor.
- ½ cup unsalted butter, softened (for frosting): Creates a luscious base for the frosting’s creamy texture.
- 2 cups powdered sugar: Sweetens and thickens the frosting to perfect spreadability.
- 1 tablespoon lemon juice (for frosting): Balances sweetness with fresh citrus tang.
- 1 teaspoon lemon zest (for frosting): Packs intense lemon flavor into every frosting bite.
- 1–2 tablespoons heavy cream or milk: Adjusts the frosting’s consistency for easy spreading.
How to Make Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting Recipe
Step 1: Prepare Your Oven and Dry Ingredients
Start by heating your oven to 350°F (175°C). Line a 12-cup muffin tin with cupcake liners, which will ensure easy removal and a tidy presentation. In a medium bowl, whisk together the all-purpose flour, baking powder, and salt—this ensures even distribution for a light, fluffy cupcake base.
Step 2: Cream Butter and Sugar, Then Add Eggs and Flavorings
Using a large bowl, beat the softened butter with the sugar until the mixture is pale and fluffy—this step is key for a tender crumb. Add the eggs one at a time, beating well after each addition to fully incorporate them. Then, stir in the vanilla extract, lemon zest, and lemon juice to infuse the batter with bright, zesty flavors.
Step 3: Combine Wet and Dry Ingredients Alternately
Add your dry ingredients to the wet mixture in three parts, alternating with milk in two additions, starting and finishing with the dry. Gently mix until just combined to avoid overworking the batter, which keeps your cupcakes wonderfully light.
Step 4: Prepare the Cheesecake Filling
In a small bowl, beat together the softened cream cheese, granulated sugar, and vanilla extract until the mixture is smooth and creamy. This luscious filling will be the delightful surprise right in the center of each cupcake.
Step 5: Fill Your Cupcake Liners
Spoon about 1 tablespoon of cupcake batter into the bottom of each liner. Then, dollop 1 teaspoon of the cheesecake filling right into the center. Cover with more cupcake batter until each liner is approximately three-quarters full to ensure a perfect rise around the creamy center.
Step 6: Bake Your Cupcakes to Perfection
Bake for 18 to 22 minutes, or until a toothpick inserted into the cake part (careful not to hit the cheesecake center) comes out clean. Cool cupcakes completely on a wire rack before moving on to frosting, so your creamy filling and cake set beautifully without melting the frosting.
Step 7: Make the Lemon Frosting and Decorate
Beat softened butter in a large bowl until creamy. Gradually incorporate powdered sugar, then mix in lemon juice and lemon zest for that perfect citrus tang. Add 1 to 2 tablespoons of heavy cream or milk as needed to create a smooth, spreadable frosting. Once the cupcakes are fully cooled, spread them generously with the lemon frosting and optionally garnish with extra lemon zest or a thin slice of lemon for a cheerful finishing touch.
How to Serve Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting Recipe

Garnishes
The simplest garnish options can truly elevate your presentation. Think bright lemon zest spirals or delicate thin lemon slices perched atop the frosting. For a bit of flair and texture, a light dusting of powdered sugar or a sprinkle of finely chopped pistachios add an elegant contrast and a subtle crunch.
Side Dishes
These cupcakes are a star on their own, but they pair wonderfully with refreshing sides like a crisp berry salad or a simple bowl of fresh fruit. A light iced tea or a sparkling lemonade complements the lemon flavor beautifully, rounding out the refreshing dessert experience.
Creative Ways to Present
For a fun party twist, arrange the cupcakes on a tiered cake stand garnished with fresh flowers or lemon branches. You can also serve these cupcakes in clear cellophane bags tied with a pretty ribbon for sweet party favors or gift ideas. For a stunning dessert table, layer cupcake stands with mixed citrus fruits to highlight the bright lemon flavors.
Make Ahead and Storage
Storing Leftovers
After baking and frosting, store leftover cupcakes in an airtight container in the refrigerator for up to four days. This keeps the cheesecake filling fresh and the frosting perfect. For the best eating experience, allow them to come to room temperature before serving to soften the frosting and enhance flavors.
Freezing
If you want to keep these delightful treats longer, freeze unfrosted cupcakes by wrapping them individually in plastic wrap and placing them in a sealed container. Freeze for up to three months. Thaw completely at room temperature before frosting and serving to maintain that fresh-baked taste and creamy center.
Reheating
Since these cupcakes are best enjoyed cool or at room temperature, avoid reheating to preserve the texture of the cheesecake filling and frosting. Simply let refrigerated cupcakes sit out for 20 minutes before serving for ideal flavor and softness.
FAQs
Can I use low-fat cream cheese in this recipe?
While you can use low-fat cream cheese, it may affect the creamy texture and richness of your cheesecake filling. For the best luscious results, full-fat cream cheese is recommended.
How can I make these cupcakes more intensely lemony?
For an extra lemon punch, you can add a few drops of lemon extract to both the cupcake batter and the frosting. Just be careful not to overdo it, as lemon extract is very concentrated.
Is it okay to use a hand mixer instead of a stand mixer?
Absolutely! A hand mixer works perfectly fine for creaming butter, sugar, and mixing your batter and frosting. Just make sure to beat until you achieve the right fluffy texture at each step.
Can I substitute the whole milk with a dairy-free alternative?
Yes, you can substitute whole milk with unsweetened almond milk or coconut milk. This may slightly alter the flavor and texture but will still keep your cupcakes moist and delicious.
Why did my cheesecake filling sink to the bottom?
If your cheesecake filling sank, it might be because it was added before the cupcake batter was thick enough or overfilled. Try chilling the filling slightly before adding, and don’t overfill the liners to give the batter enough structure to hold the filling in place during baking.
Final Thoughts
There is something truly magical about the Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting Recipe—they combine familiar, fresh flavors with a show-stopping creamy center that makes every bite feel special. Whether you’re baking for family, friends, or a celebration, these cupcakes bring a joyful burst of sunshine and indulgence to the table. I can’t recommend trying this recipe enough; once you do, it’s bound to become one of your go-to favorites for lemon desserts!
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
These Cheesecake Stuffed Lemon Cupcakes feature a moist lemon-infused cake filled with a creamy cheesecake center and topped with a tangy lemon frosting. Perfect for spring or any occasion that calls for a delightful citrusy dessert with rich, creamy texture.
Ingredients
For the Cupcakes:
- 1 ½ cups all-purpose flour
- 1 ½ teaspoons baking powder
- ¼ teaspoon salt
- ½ cup unsalted butter, softened
- 1 cup granulated sugar
- 2 large eggs
- 1 teaspoon vanilla extract
- 2 tablespoons lemon zest
- 2 tablespoons lemon juice
- ½ cup whole milk
For the Cheesecake Filling:
- 6 ounces cream cheese, softened
- 3 tablespoons granulated sugar
- 1 teaspoon vanilla extract
For the Lemon Frosting:
- ½ cup unsalted butter, softened
- 2 cups powdered sugar
- 1 tablespoon lemon juice
- 1 teaspoon lemon zest
- 1–2 tablespoons heavy cream or milk
Instructions
- Preheat and Prepare: Preheat oven to 350°F (175°C). Line a 12-cup muffin tin with cupcake liners to prevent sticking.
- Mix Dry Ingredients: In a medium bowl, whisk together the all-purpose flour, baking powder, and salt to evenly disperse the leavening agents.
- Cream Butter and Sugar: In a separate large bowl, beat the softened butter and granulated sugar until the mixture is light and fluffy, incorporating air for a soft cupcake texture.
- Add Eggs and Flavorings: Add the eggs one at a time to the butter-sugar mixture, beating well after each addition. Then mix in the vanilla extract, lemon zest, and lemon juice to infuse bright citrus flavor.
- Combine Wet and Dry Ingredients: Alternately add the dry ingredients and whole milk to the wet mixture, starting and ending with the dry ingredients. Mix just until combined to avoid overworking the batter and toughening the cupcakes.
- Prepare Cheesecake Filling: In a small bowl, beat the softened cream cheese, granulated sugar, and vanilla extract until smooth and creamy, creating the luscious filling.
- Fill Cupcake Liners: Spoon about 1 tablespoon of cupcake batter into each liner. Add 1 teaspoon of the cheesecake filling in the center of each, then cover with more batter until each cup is approximately ¾ full.
- Bake: Bake in the preheated oven for 18 to 22 minutes, or until a toothpick inserted into the cake portion (not the cheesecake center) comes out clean, indicating doneness.
- Cool: Allow cupcakes to cool completely in the tin before frosting, ensuring the frosting does not melt.
- Make Lemon Frosting: Beat the softened butter until creamy. Gradually add powdered sugar, mixing well. Stir in lemon juice and lemon zest for flavor. Add heavy cream or milk 1 tablespoon at a time until the frosting reaches a spreadable consistency.
- Frost and Garnish: Spread the lemon frosting on the cooled cupcakes. Optionally garnish with extra lemon zest or a thin lemon slice for an elegant finishing touch.
Notes
- For a more intense lemon flavor, substitute lemon extract in the cupcakes or frosting.
- Store cupcakes in the refrigerator for up to 4 days to maintain freshness.
- Bring cupcakes to room temperature before serving for the best texture and flavor experience.