If you’re looking for a dessert that brings together the bright zing of lemon with the creamy indulgence of cheesecake, you’ll fall head over heels for this Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting Recipe. These delightful cupcakes are bursting with fresh lemon flavor, from the tender cake to the luscious cheesecake center, all crowned with a smooth, tangy lemon frosting. Bright, creamy, and just the right amount of sweet, this recipe is a guaranteed crowd-pleaser that will quickly become one of your favorites to bake and share.

Ingredients You’ll Need
Each ingredient in this Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting Recipe plays a vital role in creating the perfect balance of flavors and textures. From flour that builds structure to fresh lemon juice that delivers brightness, these simple yet essential components come together beautifully.
- All-purpose flour: Provides the sturdy yet tender base for the cupcakes.
- Granulated sugar: Sweetens and helps to create a moist crumb.
- Unsalted butter: Adds richness and a tender texture.
- Milk: Keeps the batter moist and blends flavors smoothly.
- Baking powder: Ensures the cupcakes rise perfectly light and fluffy.
- Salt: Balances and enhances the sweetness.
- Vanilla extract: Adds warmth and depth to the lemon flavor.
- Large eggs: Bind the ingredients and add moisture and structure.
- Lemon zest: Provides concentrated lemon oil for an aromatic punch.
- Fresh-squeezed lemon juice: Delivers fresh citrus acidity for brightness.
- Instant cheesecake pudding mix: Creates that delicious cheesecake center with minimal fuss.
- Softened cream cheese: Makes the frosting creamy, tangy, and irresistible.
- Powdered sugar: Sweetens the frosting and ensures a smooth finish.
- Yellow gel food coloring (optional): Adds a vivid pop of sunshine to your frosting for eye appeal.
How to Make Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting Recipe
Step 1: Prepare the Cupcake Batter
Start by preheating your oven and lining your muffin tin with cupcake liners. In a large bowl, whisk together the flour, baking powder, and salt. In a separate bowl, cream the butter and sugar until fluffy, then add eggs one at a time, mixing well after each addition. Stir in the vanilla extract, lemon zest, and lemon juice before alternating adding the dry ingredients and milk, beginning and ending with the dry. This creates a smooth batter packed with fresh lemon flavor.
Step 2: Mix the Cheesecake Filling
In a medium bowl, combine the instant cheesecake pudding mix with milk and whisk until slightly thickened. This will be the luscious filling inside your cupcakes that gives you a creamy surprise with every bite.
Step 3: Fill the Cupcake Liners
Fill each cupcake liner halfway with batter. Then, add a generous spoonful of the cheesecake pudding mixture, ensuring the center will be creamy and oozy. Top off with more batter until each liner is about two-thirds full. This layering is what makes these cupcakes shine.
Step 4: Bake
Bake your cupcakes in the preheated oven for about 18 to 22 minutes, or until a toothpick inserted near the edge (avoiding the filling) comes out clean. Let them cool in the pan for a few minutes before transferring to a wire rack to complete cooling—cool cupcakes ensure your frosting doesn’t melt.
Step 5: Prepare the Lemon Frosting
Beat the softened butter and cream cheese together until smooth and creamy. Gradually add powdered sugar, and mix until light and fluffy. Stir in fresh lemon juice and lemon zest for that perfect tang. If desired, add a touch of yellow gel food coloring to brighten the frosting to a sunny hue.
Step 6: Frost Your Cupcakes
Once the cupcakes are completely cool, generously frost each one with your luscious lemon frosting. Be creative—use a piping bag, a knife, or a spatula to decorate. Your effort will shine through every swirl and dollop.
How to Serve Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting Recipe

Garnishes
Enhance the visual appeal and flavor by adding delicate garnishes. Thin lemon slices, edible flowers, or a light dusting of lemon zest on top of the frosting bring freshness and charm to your cupcakes, making them irresistible on any dessert table.
Side Dishes
Pair these cupcakes with simple sides like fresh berries, a dollop of whipped cream, or a light sparkling lemonade. These complements allow the flavors to shine while keeping the overall dessert experience bright and refreshing.
Creative Ways to Present
For a fun twist, serve your Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting Recipe in mini paper boxes or atop pretty cake stands. Add coordinating napkins or pastel plates to bring cheerful vibes to your gathering. Presentation goes a long way in elevating the homemade charm!
Make Ahead and Storage
Storing Leftovers
Store leftover cupcakes in an airtight container in the refrigerator to keep the creamy filling and frosting fresh. They will stay delicious for up to 3 days while maintaining their moist texture and bright lemon flavor.
Freezing
You can freeze undecorated cupcakes for up to 2 months by wrapping them tightly in plastic wrap, then placing in a freezer bag. Defrost overnight in the fridge before frosting to preserve texture and taste. Avoid freezing fully frosted cupcakes as the frosting’s texture can change.
Reheating
If you prefer your cupcakes warmed, remove frosting and gently warm the cupcake in the microwave for about 10 seconds. Add the frosting back or enjoy as is for a gooey, slightly melted treat. This little step brings out the creaminess of the cheesecake center beautifully.
FAQs
Can I use regular lemon pudding instead of cheesecake pudding mix?
While regular lemon pudding will add lemony flavor, the instant cheesecake pudding mix provides a richer, creamier texture that’s essential for the cheesecake center. Using it is recommended for authentic results.
How do I prevent the cheesecake filling from leaking during baking?
Fill the cupcake liners carefully, layering the batter and filling evenly and avoid overfilling the cups. Baking at the right temperature ensures everything sets properly without oozing over.
Can these cupcakes be made gluten-free?
Yes! Substituting all-purpose flour with a high-quality gluten-free flour blend that measures cup-for-cup will work well. Just be mindful of texture differences and consider adding a binder if your blend doesn’t include one.
Is it okay to use bottled lemon juice instead of fresh?
Fresh lemon juice really makes a difference in brightness and freshness in this recipe. If using bottled juice, choose a high-quality one, but fresh is always best for that vibrant lemon pop.
How long does it take to make this recipe from start to finish?
This Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting Recipe typically takes about 45 minutes, including baking and frosting time. It’s a quick project that delivers impressive results every time.
Final Thoughts
Nothing beats the joy of biting into a cupcake that surprises you with a creamy cheesecake center, lively lemon flavors, and velvety frosting. This Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting Recipe is sure to brighten your baking routine and bring smiles to everyone who tastes them. Go ahead, gather your ingredients, and make a batch today—you won’t regret it!
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Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting Recipe
- Prep Time: 15 minutes
- Cook Time: 20 minutes
- Total Time: 35 minutes
- Yield: 24 servings
- Category: Dessert
- Method: Baking
- Cuisine: American
Description
These Cheesecake Stuffed Lemon Cupcakes are a delightful treat combining zesty lemon flavor with rich creamy cheesecake filling, topped with smooth lemon frosting. Perfect for parties or a refreshing dessert, these cupcakes boast a moist texture infused with fresh lemon juice and zest, complemented by a luscious cheesecake center and a tangy lemon buttercream frosting.
Ingredients
Cupcakes
- 2 1/4 cups all-purpose flour
- 1 2/3 cups granulated sugar
- 2/3 cup unsalted butter, softened
- 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 fresh-squeezed lemon juice
Cheesecake Filling
- 3.3 ounces instant cheesecake pudding mix
- 1 1/2 cups milk
Lemon Frosting
- 1/2 cup unsalted butter, softened
- 4 ounces cream cheese, softened
- 16 ounces powdered sugar, sifted
- 1 tablespoon fresh-squeezed lemon juice
- 1 teaspoon lemon zest
- Yellow gel food coloring (optional)
Instructions
- Prepare the Cupcake Batter: Preheat your oven to 350°F (175°C) and line a muffin tin with cupcake liners. In a large mixing bowl, combine the flour, sugar, baking powder, and salt. In a separate bowl, whisk together the softened butter, milk, eggs, lemon zest, lemon juice, and vanilla extract. Gradually add the wet ingredients to the dry ingredients and mix until just combined, being careful not to overmix to keep the cupcakes light and fluffy.
- Prepare the Cheesecake Filling: In another bowl, whisk the instant cheesecake pudding mix with 1 1/2 cups of milk until it thickens. This will be the creamy filling to stuff inside the cupcakes.
- Assemble the Cupcakes: Fill each cupcake liner halfway with the lemon cupcake batter. Add about a tablespoon of the cheesecake pudding mixture in the center, then cover with more cupcake batter to fill 3/4 full. This layering ensures a delicious cheesecake center baked inside each cupcake.
- Bake the Cupcakes: Place the muffin tin in the preheated oven and bake for 18-22 minutes, or until a toothpick inserted into the cupcake (avoiding the filling) comes out clean. Once baked, remove from oven and allow cupcakes to cool completely on a wire rack before frosting.
- Make the Lemon Frosting: In a mixing bowl, beat the softened butter and cream cheese until smooth and creamy. Gradually add sifted powdered sugar, continuing to beat until well combined. Stir in lemon juice, lemon zest, and optional yellow gel food coloring to create a bright, tangy frosting.
- Frost and Serve: Once cupcakes are completely cool, pipe or spread the lemon frosting generously on top of each cupcake. Decorate as desired and enjoy the refreshing combination of lemon and creamy cheesecake flavors.
Notes
- Use room temperature ingredients for the best texture and mixing results.
- Do not overmix the batter to keep cupcakes tender and moist.
- Ensure cupcakes are fully cooled before frosting to prevent melting.
- Optional: Add a sprinkle of lemon zest or small edible flowers for garnish.
- These cupcakes can be stored in an airtight container in the refrigerator for up to 3 days.

