If you are on the hunt for a dessert that bursts with bright citrus flavor and creamy indulgence, these Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting Recipe will absolutely delight your taste buds. Imagine moist lemon-infused cupcakes hiding a luscious cheesecake center, all topped with tangy lemon frosting that is perfectly sweet and smooth. This recipe combines the best of lemon’s sunshine zing and cheesecake’s velvety richness into a handheld treat that’s as fun to eat as it is to make. Once you take your first bite, these cupcakes will quickly become a favorite dessert for any season, bringing a little zest and a lot of joy to your table.

Ingredients You’ll Need
Gathering simple, fresh ingredients is key to nailing the perfect balance of flavors and textures in this recipe. Each component plays an essential role, from the tender crumb of the cupcake to the creamy cheesecake pocket and that irresistibly fluffy lemon frosting. Here’s everything you need to create magic in your kitchen.
- All-purpose flour: The foundation for your cupcakes’ soft, yet sturdy texture.
- Baking powder and baking soda: Help your cupcakes rise perfectly light and tender.
- Salt: Balances out the sweetness and enhances the other flavors.
- Unsalted butter (softened): Adds richness and moisture for a melt-in-your-mouth crumb.
- Granulated sugar: Sweetens the cupcakes and cheesecake filling just right.
- Large eggs: Bind the ingredients together and add structure.
- Lemon zest and fresh lemon juice: Pack in that signature bright, fresh lemon flavor.
- Vanilla extract: Adds a warm, sweet undertone.
- Sour cream: Keeps the cupcakes moist and tender with a subtle tang.
- Milk: Helps balance the batter’s consistency for the perfect rise.
- Cream cheese (softened): Creates the creamy, dreamy cheesecake filling inside.
- Powdered sugar: Makes the lemon frosting silky smooth and sweet.
- Heavy cream: Fluffs up the frosting for that light and luscious texture.
- Pinch of salt: Enhances the frosting’s flavors and balances sweetness.
How to Make Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting Recipe
Step 1: Prep Your Oven and Ingredients
Start by preheating your oven to 350°F (175°C). Line a 12-cup muffin pan with paper liners to make clean removal and serving a breeze. Then, whisk together the flour, baking powder, baking soda, and salt in a medium bowl — this dry mix will help your cupcakes rise beautifully.
Step 2: Create the Lemon Cupcake Batter
In a large mixing bowl, beat the softened butter and granulated sugar together until the mixture is light and fluffy — this is the secret to tender cupcakes. Add the eggs one at a time, making sure each is well incorporated before adding the next. Stir in the bright lemon zest, fresh lemon juice, and vanilla extract. Finally, gently mix in the sour cream and milk, which keeps your cupcakes moist and tender. Gradually fold in the dry ingredient mixture just until combined, careful not to overmix!
Step 3: Make the Cheesecake Filling
Using a small bowl, beat the softened cream cheese with sugar and vanilla extract until you have a smooth, creamy filling. This filling is what makes these cupcakes extra special, so make sure it is thick and luscious for that perfect surprise center.
Step 4: Assemble and Bake
Fill each cupcake liner about one-third full with your lemon batter. Then, drop a heaping teaspoon of cheesecake filling into the center of each cupcake. Cover the filling with more lemon batter until the liner is roughly two-thirds full. Bake for 18 to 22 minutes, or until the tops spring back to the touch and a toothpick inserted near the edge comes out clean. Once baked, transfer the cupcakes to a wire rack and allow them to cool completely.
Step 5: Whip Up the Lemon Frosting
For the frosting, beat the butter until creamy and smooth. Add the powdered sugar one cup at a time while mixing on low speed to avoid a sugar cloud in your kitchen! Add fresh lemon juice, lemon zest, a pinch of salt, and heavy cream as needed to achieve a fluffy, luscious texture. Beat on high for a few more minutes until light and fluffy. Once your cupcakes are completely cool, generously frost each one with your homemade lemon frosting.
How to Serve Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting Recipe

Garnishes
Adding a little extra pizzazz on top makes these cupcakes as pretty as they are delicious. Try garnishing with a small sprinkle of fresh lemon zest, a thin lemon slice, or even some edible flowers to brighten up the presentation. These subtle touches make the cupcakes look irresistible and emphasize their fresh lemon character.
Side Dishes
Serve these cupcakes alongside a refreshing cup of iced tea or a zesty lemonade to amplify the citrus experience. If you want to keep things light, pair them with a simple fresh fruit salad featuring berries and mint. The balance of flavors will make your dessert experience feel complete and well thought out.
Creative Ways to Present
For parties or special occasions, consider displaying your Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting Recipe on a tiered dessert stand or in pretty pastel-colored wrappers to evoke the feeling of springtime and sunshine. You could even pipe the frosting in fun swirls or rosettes, or add a dusting of powdered sugar for an elegant touch that will wow your guests.
Make Ahead and Storage
Storing Leftovers
You can store your cupcakes in an airtight container in the refrigerator for up to 4 days. Because of the cream cheese filling and frosting, refrigeration is essential to keep them fresh and safe to eat. Just let them come to room temperature before serving for the best flavor and texture.
Freezing
These lemon cupcakes freeze beautifully! Freeze unfrosted cupcakes in a single layer on a baking sheet, then transfer to an airtight container or freezer bag once frozen solid. To thaw, leave them in the fridge overnight. You can also freeze frosted cupcakes but be aware the frosting may slightly change texture after thawing.
Reheating
For the best eating experience, allow refrigerated cupcakes to come to room temperature naturally. Avoid microwaving as this can melt the frosting and affect texture. If you want a warm cupcake, gently warm the unfrosted cupcake only, then add frosting fresh before serving.
FAQs
Can I use lemon extract instead of fresh lemon juice?
Yes, lemon extract can be used in place of fresh lemon juice for a more concentrated lemon flavor. Just be sure to use it sparingly since it is more potent than fresh juice, as noted in the recipe tips.
How do I ensure the cheesecake filling stays in the center?
Filling the cupcake liners first with a layer of batter, then adding a teaspoon of thick cheesecake filling before topping off with more batter helps keep it perfectly centered during baking.
Can I make these cupcakes dairy-free?
While this recipe relies on dairy for its rich texture and flavor, you could experiment with dairy-free cream cheese and butter substitutes. Keep in mind that it may slightly change the texture and taste.
What is the best way to pipe the lemon frosting?
A large star tip or round tip works wonderfully for this frosting, allowing you to create pretty rosettes or swirls. Make sure your frosting is at a spreadable but firm consistency to hold its shape.
Can I double this recipe for a larger batch?
Absolutely! This recipe scales well. Just be sure to use an appropriate size baking pan or bake in batches and adjust baking time accordingly.
Final Thoughts
There is something truly joyful about biting into a cupcake that surprises you with a creamy cheesecake center and finishes with a burst of lemony freshness. I encourage you to give this Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting Recipe a try — it’s a delightful treat that’s sure to brighten up your dessert lineup and bring smiles all around. These cupcakes combine familiar flavors into a memorable dessert that feels both special and comforting, making them perfect for any occasion.
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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 with Lemon Frosting combine a moist and tangy lemon cupcake with a luscious, creamy cheesecake center, topped with a bright, fluffy lemon frosting. Perfectly balanced for spring or any occasion, these delightful treats offer a burst of citrus flavor with a rich, creamy surprise inside.
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
- Prepare the Oven and Dry Ingredients: Preheat the oven to 350°F (175°C). Line a 12-cup muffin pan with paper liners. In a medium bowl, whisk together the flour, baking powder, baking soda, and salt until evenly combined.
- Mix Wet Ingredients: In a large mixing bowl, beat the softened butter and granulated sugar until the mixture is light and fluffy. Add the eggs one at a time, beating thoroughly after each addition. Incorporate the lemon zest, fresh lemon juice, and vanilla extract next, blending well.
- Combine Batter: Stir in the sour cream and milk until the mixture is smoothly combined. Gradually add the dry ingredients to this wet mixture, folding gently and mixing just until incorporated to avoid overmixing.
- Make Cheesecake Filling: In a separate small bowl, beat the softened cream cheese, granulated sugar, and vanilla extract together until the filling is smooth and creamy without lumps.
- Assemble Cupcakes: Fill each cupcake liner about one-third full with the lemon batter. Carefully add about one heaping teaspoon of cheesecake filling to the center of each liner. Top this with more lemon batter until each liner is about two-thirds full, completely covering the cheesecake layer.
- Bake: Place the muffin pan in the oven and bake for 18-22 minutes. The cupcakes are done when their tops spring back when lightly touched and a toothpick inserted near the edge comes out clean. Remove from oven and allow to cool completely on a wire rack.
- Make Lemon Frosting: Beat the softened butter until creamy. Gradually add the powdered sugar one cup at a time, mixing on low speed after each addition. Add the lemon juice, lemon zest, a pinch of salt, and heavy cream as needed to achieve the desired consistency. Beat everything on high speed for 2-3 minutes until the frosting is fluffy.
- Frost and Garnish: Once cupcakes have cooled completely, frost them generously with the lemon frosting. Optionally, garnish with additional lemon zest or small lemon slices for an elegant presentation.
Notes
- Ensure the cream cheese filling is thick and not runny to maintain a good stuffed center.
- You can substitute some of the fresh lemon juice with lemon extract for a more intense lemon flavor.
- Store cupcakes in the refrigerator for up to 4 days to keep them fresh.

