If you’re on the hunt for a dessert that perfectly balances tangy brightness with creamy indulgence, look no further than this dazzling Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting Recipe. These cupcakes are not just your everyday lemon treats; each one hides a luscious cheesecake center that melts in your mouth, topped with a zesty lemon frosting that elevates every bite. Whether it’s a sunshine-filled brunch, a special celebration, or just a treat-yourself moment, this recipe brings a burst of flavor and delightful texture that’s impossible to resist.

Ingredients You’ll Need
Gathering the right ingredients is half the magic, and this recipe shines because of its simple yet thoughtful components. Each element plays its part — from the fresh lemon juice adding that fresh zing to the creamy butter imparting richness, plus the delicate cheesecake pudding mix for an unforgettable surprise inside.
- All-purpose flour (2 ¼ cups): Provides the perfect structure for tender cupcakes with a soft crumb.
- Granulated sugar (1 ⅔ cups): Sweetens perfectly without overpowering the lemon’s natural tartness.
- Unsalted butter (2/3 cup plus 1/2 cup softened): Adds a rich, creamy texture and helps create a moist cupcake and smooth frosting.
- Milk (1 ¼ cups plus 1 ½ cups): Keeps the cupcakes light and the filling silky smooth.
- Baking powder (4 teaspoons): Ensures your cupcakes rise beautifully and stay fluffy.
- Salt (1 teaspoon): Balances the sweetness and enhances the overall flavors.
- Vanilla extract (1 teaspoon): Brings depth and warmth to the lemon-forward batter.
- Large eggs (3): Bind everything together while giving stability and richness.
- Lemon zest (1 teaspoon plus 1 teaspoon for frosting): Infuses a bright, aromatic note that wakes up the palate.
- Fresh-squeezed lemon juice (1/4 cup plus 1 tablespoon for frosting): The star player, providing vibrant citrus flavor in both cupcakes and frosting.
- Instant cheesecake pudding mix (3.3 ounces): Creates that creamy, dreamy cheesecake filling inside each cupcake.
- Cream cheese (4 ounces, softened): Smooth and tangy, essential for luscious frosting.
- Powdered sugar (16 ounces, sifted): Gives the frosting its sweet, velvety texture without any graininess.
- Yellow gel food coloring (optional): For that sunny, cheerful hue that makes these cupcakes visually irresistible.
How to Make Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting Recipe
Step 1: Prepare the Cupcake Batter
Start by preheating your oven to 350°F (175°C) and lining two muffin tins with cupcake liners. In a large bowl, whisk together the flour, baking powder, and salt to ensure even distribution. In a separate bowl, beat the butter and sugar until light and fluffy — this step is crucial for creating an airy texture. Add the eggs one at a time, beating well after each addition, then stir in the vanilla, lemon zest, and lemon juice. Alternately add the dry ingredients and milk, beginning and ending with dry, mixing just until combined to avoid overworking the batter.
Step 2: Mix the Cheesecake Filling
In another bowl, whisk the instant cheesecake pudding mix with 1 ½ cups of milk until it thickens — typically around two minutes. This mixture will be your luscious, creamy filling that surprises inside every cupcake, giving a smooth and tangy contrast to the lemon cake.
Step 3: Fill the Cupcake Liners
Using a spoon or an ice cream scoop, fill each cupcake liner halfway with batter. Add a heaping tablespoon of the cheesecake pudding mixture to the center, then top with more cupcake batter until the liner is about two-thirds full. This way, every bite gets that delightful cheesecake heart without overpowering the lemon flavor.
Step 4: Bake the Cupcakes
Bake in the preheated oven for about 20 to 25 minutes or until a toothpick inserted near the edge of the cupcake comes out clean. Allow them to cool completely in the pan before transferring to a wire rack — this prevents the cheesecake filling from oozing out prematurely and lets the cupcakes set perfectly.
Step 5: Prepare the Lemon Frosting
Beat softened butter and cream cheese together until smooth and creamy. Gradually add powdered sugar, lemon juice, and lemon zest, mixing thoroughly after each addition. Add a few drops of yellow gel food coloring if you want that classic lemony look. The frosting should be fluffy and bright, complementing the cupcakes’ soft texture and tangy filling.
Step 6: Frost the Cupcakes
Once cupcakes are completely cooled, generously frost the tops using a piping bag or a simple spatula. You can get creative here by swirling the frosting into cheerful peaks that invite eager bites and add visual charm.
How to Serve Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting Recipe

Garnishes
To make these cupcakes look as fantastic as they taste, consider adding thin lemon slices, edible flowers, or candied lemon peel on top. These not only add a pop of color and fresh scent but also hint at the zesty delights waiting inside.
Side Dishes
These cupcakes shine best on their own, but pairing them with a simple fresh berry salad or a light green tea provides a refreshing contrast. The mild bitterness of tea balances the sweet and tart flavors, making each bite even more enjoyable.
Creative Ways to Present
For a party or special occasion, arrange your cheesecake stuffed lemon cupcakes on a tiered stand with lemon wedges and miniature mint sprigs scattered around. You can even serve them with small spoons for guests to scoop the creamy centers with ease, turning each serving into an interactive experience.
Make Ahead and Storage
Storing Leftovers
Store leftover cupcakes in an airtight container in the refrigerator for up to 3 days. The cool environment helps keep the cream cheese frosting fresh and the cheesecake filling intact without drying out the cupcakes.
Freezing
If you want to save some for later, freeze unfrosted cupcakes in a single layer on a baking sheet. Once solid, transfer them to a freezer bag or container. Frost them after thawing in the fridge overnight for best results. The texture holds up well, so you’ll get nearly the same delightful experience anytime.
Reheating
To gently revive your cupcakes after refrigeration, let them come to room temperature for about 30 minutes. Avoid microwaving as it can affect the frosting and filling texture. Room temp brings out the full flavor and creaminess without any unwanted melting or separation.
FAQs
Can I use regular lemon pudding instead of instant cheesecake pudding mix?
While regular lemon pudding will add more lemon flavor, it won’t provide the rich, creamy cheesecake texture that makes these cupcakes so irresistible. The cheesecake pudding mix is key for that luscious surprise inside.
Is it possible to make these cupcakes dairy-free?
Yes, but you’ll need suitable substitutes. Use dairy-free butter and milk alternatives, and opt for a dairy-free cream cheese brand. Keep in mind the texture and flavor might differ slightly, but they can still be delicious!
Can I make these cupcakes ahead of time for a party?
Absolutely! They actually benefit from a few hours in the fridge to let the flavors meld. Just frost them closer to serving to keep the frosting looking fresh and fluffy.
How do I prevent the cheesecake filling from leaking during baking?
Make sure you don’t overfill the cupcake liners and keep the cheesecake filling portion moderate. Chilling the filling before scooping into the batter can also help it hold shape better while baking.
What’s the best way to get a bright yellow frosting without adding too much food coloring?
Using fresh lemon juice and zest naturally enhances the color, so start there. Then add just a tiny dab of yellow gel food coloring, as it’s more concentrated and takes less to achieve a vibrant hue without affecting flavor.
Final Thoughts
There’s nothing quite like biting into a cupcake that surprises you with a creamy cheesecake center and finishes with a zesty lemon frosting that dances on your tongue. This Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting Recipe is a celebration of texture and flavor that’s perfect for any occasion, or even just because you deserve a little sunshine in your day. I can’t wait for you to make these and share the joy — they’re sure to become a beloved favorite in your recipe collection!
Print
Cheesecake Stuffed Lemon Cupcakes with Lemon Frosting Recipe
- Prep Time: 15 minutes
- Cook Time: 20 minutes
- Total Time: 45 minutes
- Yield: 24 cupcakes
- Category: Dessert
- Method: Baking
- Cuisine: American
Description
These Cheesecake Stuffed Lemon Cupcakes are light, moist, and bursting with fresh lemon flavor. Each cupcake features a creamy cheesecake filling and is topped with a luscious lemon frosting, making them perfect for spring celebrations or any time you want a delightful citrus dessert.
Ingredients
Cupcake Batter
- 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
- Preheat and prepare pans: Preheat your oven to 350°F (175°C). Line a muffin tin with cupcake liners.
- Make cupcake batter: In a large bowl, cream together the softened butter and granulated sugar until light and fluffy. Beat in the eggs one at a time, then add the vanilla extract, lemon zest, and lemon juice. In a separate bowl, whisk together the flour, baking powder, and salt. Alternately add the dry ingredients and milk to the butter mixture, beginning and ending with dry ingredients. Mix just until combined.
- Prepare cheesecake filling: In a medium bowl, combine the instant cheesecake pudding mix and milk. Whisk until thickened.
- Fill cupcake tins: Spoon about 1 tablespoon of cupcake batter into each liner. Add about 1 tablespoon of cheesecake filling in the center, then cover with more cupcake batter until the cups are about 2/3 full.
- Bake: Bake for 18-22 minutes or until a toothpick inserted into the cake (avoiding the filling) comes out clean. Remove from oven and allow cupcakes to cool completely on a wire rack.
- Make lemon frosting: In a large bowl, beat together softened butter and cream cheese until smooth and creamy. Gradually add powdered sugar, then beat in lemon juice, lemon zest, and optional yellow gel food coloring until frosting is smooth and fluffy.
- Frost cupcakes: Once cupcakes are completely cooled, frost the tops generously with the lemon frosting using a spatula or piping bag.
- Serve and store: Serve immediately or refrigerate in an airtight container for up to 3 days. Bring to room temperature before serving for best flavor and texture.
Notes
- Make sure cupcakes are fully cooled before frosting to prevent melting.
- You can substitute milk with buttermilk for a tangier cupcake.
- Use fresh lemon juice for best citrus flavor.
- Store cupcakes in the refrigerator due to cream cheese frosting.
- Let refrigerated cupcakes come to room temperature before serving for optimal taste.

