Yummy Lemon Cheesecake Cupcake Recipe

These lemon cheesecake cupcakes are the perfect bright, sweet dessert. The tangy citrus flavor is balanced out with the luscious cheesecake filling and a fluffy cupcake base.

Our perfect summer dessert is topped off with a lemon buttercream frosting that takes these cupcakes up to the next level. Adults and kids alike can enjoy the bright, light flavor of these sweet treats.

Closeup of a lemon cheesecake cupcake sitting on a lemon slice.

RELATED READING: Easy Lemon Poundcake Cookies

Lemon Cheesecake Cupcakes

Here at Ruffles and Rain Boots, we love fun and unique cupcake recipes. This dessert is taken to the next level with the cheesecake pudding filling.

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These easy to make cupcakes are packed with lemon flavor in the cupcake itself as well as the buttercream frosting. They have the perfect amount of tangy zing combined with a satisfyingly sweet flavor making them a perfect dessert for any Spring or Summer day and are much easier to make than most cheesecake recipes.

If you aren’t ready to make this recipe yet because you need to get your ingredients together, just bookmark this page so you can pop back in when you are ready.

Lemon cheesecake cupcake cut in half sitting on a white plate.

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Perfect Summer Cupcakes for a Warm Day

These delicious citrus delights are packed with lemon flavor, but the creamy cheesecake pudding filling helps to smooth down the citrus tang.

Even though this is a from scratch recipe and has three main components – cupcake base, frosting, and filling – it is still easy to make. And you can always start with my cake mix cupcake recipe base.

This versatile mini lemon cheesecake dessert is fancy enough to be served at parties and celebrations, but easy enough to whip up for your own afternoon treat.

Three lemon cheesecake cupcakes on white plates.

Tips For Making This Summer Cupcake Recipe

  • To make sure your cupcakes are light and fluffy, don’t over-mix the batter. In order to help prevent over-mixing, you should use softened butter and room temperature eggs and cream cheese.
  • Get the buttercream to YOUR perfect consistency by adding powdered sugar to thicken or stiffen it up and a splash or milk to thin. It should be able to be scooped up and only have a little droop to it so that it will pipe well and hold its shape.
  • Create the best lemon flavor with the lemon zest. Don’t skip it because it helps create a bright, vibrant flavor. For even more lemon flavor, you can brush a lemon simple syrup on top of the cupcakes before frosting.
  • If you don’t have a piping bag, scoop frosting into a zip top bag and cut off a corner (with or without a piping tip).

Ingredients For This Lemon Cheesecake Cupcake Recipe

Below are the ingredients we used to make these cupcakes. You’ll find they are all pretty simple and standard items that you are likely to already have on hand.

For the Cupcakes:

  • All-purpose Flour
  • Granulated Sugar
  • Butter
  • Milk
  • Baking Powder
  • Salt
  • Vanilla
  • Eggs
  • Lemon Zest
  • Lemon Juice
  • Jello pudding, Cheesecake Flavor

For the Frosting:

  • Butter
  • Cream Cheese
  • Powdered/Confectioners Sugar
  • Lemon Juice
  • Lemon Zest
  • Yellow Food Coloring
Ingredients for lemon cheesecake cupcakes on a white table.

How To Make Lemon Cheesecake Cupcakes

All of the steps for this recipe are detailed below. Keep this page open while baking so that you can refer to the step-by-step instructions. Or, print the recipe by scrolling down and hitting the print button.

Preheat the oven to 350 degrees Fahrenheit, place cupcake liners into your cupcake tin, and set it aside.

Bowl with eggs, butter and sugar in it.

In a large bowl, add the butter, sugar and vanilla and cream them together until light and fluffy.

Add in the eggs and combine with the creamed butter and sugar until well combined. Then, mix in the lemon juice and lemon zest and stir well.

Stirring flour into bowl with cupcake batter.

Add in the flour, salt and baking soda.

Bowl of lemon cupcake batter with spatula in the bowl.

As you stir the dry ingredients in, pour in the milk. Keep stirring everything until it is all fully combined.

Carefully scoop the cupcake batter into the lined cupcake tin filling each about halfway full.

Cupcake pan filled with cupcake batter.

Bake the cupcakes at 350 degrees Fahrenheit for 20 – 25 minutes. While cupcakes are baking, make your cheesecake filling and frosting.

To make the cheesecake filling, mix the pudding up according to the instructions on the box and then set it aside.

Mixing together lemon buttercream frosting.

To make the frosting: add softened butter and cream cheese into a large bowl and whip them together until they are creamy.

Then, gradually beat in the powdered sugar one cup at a time. The frosting should start to form stiff peaks when the consistency is thick enough.

Finally, add in the lemon zest, lemon juice and a few drops of yellow food coloring. Fold those in until they are well combined.

Spooning cheesecake filling into a lemon cupcake in a bright white home kitchen.

Once the cupcakes are cooled, use a spoon to scoop out a small amount of the cupcake from the center. Make sure that you don’t scoop all the way down to the bottom.

Then, scoop a spoonful of the cheesecake pudding into the hole in the center of each cupcake.

Piping lemon buttercream onto a lemon cupcake.

Place the lemon buttercream frosting into a piping bag fitted with a star tip. Then, carefully pipe the frosting onto the top of each cupcake in a swirl pattern.

More Cupcake Recipes You May Like

  • Blackberry Lemon Cupcakes – These fruity and sweet cupcakes are super easy to make and the flavor combination is unmatched.
  • Lime Curd Slime Cupcakes – If you want to impress the short stacks in your life, make these slime cupcakes, friend. They’ll go wild.
  • Blueberry Cream Cheese Cupcakes
  • Banana Cream Pie Cupcakes – yet another filled cupcake to try out, this one is a cupcake version of a classic pie flavored dessert. The fluffy banana cupcakes are filled with banana pudding and topped with whipped topping and crushed vanilla wafers.

Please Save or Share This Easy Cupcake Recipe

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Lemon cheesecake cupcake with a lemon wedge on top.
Yield: 24

Lemon Cheesecake Cupcake Recipe

Closeup of a lemon cheesecake cupcake sitting on a lemon slice.

These lemon cheesecake cupcakes are the perfect combination of tangy citrus and sweet, creamy cheesecake flavors. The moist lemon cupcake base is filled with cheesecake pudding making. They are topped off with a zesty lemon buttercream frosting which make these homemade cupcakes the perfect addition for any Spring or Summer celebration.

Prep Time 20 minutes
Cook Time 25 minutes
Additional Time 30 minutes
Total Time 1 hour 15 minutes


For the Lemon Cheesecake Cupcakes

  • 2 1/4 cups all-purpose flour
  • 1 2/3 cups granulated sugar
  • 2/3 cups butter
  • 2 3/4 cups milk
  • 4 teaspoons baking powder
  • 1 teaspoon salt
  • 1 teaspoon vanilla
  • 3 eggs
  • 1 teaspoon lemon zest
  • 1/4 cup lemon juice
  • 3.3 oz of Jello pudding, cheesecake flavor

For the Lemon Buttercream Frosting

  • 1 stick of butter
  • 4 oz cream cheese
  • 16 - 20 oz powdered sugar
  • 1 tablespoon lemon juice
  • 1 teaspoon lemon zest
  • yellow food coloring


  1. Preheat the oven to 350 degrees Fahrenheit. Place cupcake liners in your cupcake tin and set aside.
  2. In a large bowl, cream together butter, sugar and vanilla. They should be light and fluffy when done, this usually takes 1 - 3 minutes.
  3. Add in the eggs and mix well until it is fully combined.
  4. Next, add in the lemon juice and lemon zest. Stir together until they are well combined.
  5. Add in the flour, baking powder and salt. As you stir in the dry goods, add in the milk and keep stirring until fully combined.
  6. Pour cupcake batter into the lined baking tins. They should be about 1/2 full.
  7. Bake at 350 degrees for 20 - 25 minutes.
  8. While cupcakes are baking, make your frosting and cheesecake filling.
  9. To make the cheesecake filling. Mix the pudding mix and milk according to the instructions on the box and set aside.
  10. To make the frosting, add softened butter and cream cheese to a large bowl and whip them until they are creamy.
  11. Then, gradually beat in the powdered sugar, adding one cup at a time. Frosting should be stiff enough that you can scoop it without it falling off a spoon.
  12. Finally, add lemon juice, lemon zest and a few drops of yellow food coloring. Fold them in until well incorporated.
  13. Once cupcakes are done and cooled, use a small spoon and scoop out the center of the cupcake. Be sure not to go all the way through the bottom of the cupcake.
  14. Fill the whole in the cupcake with a spoonful of cheesecake pudding.
  15. Scoop the lemon buttercream frosting into a piping bag with a star tip. Pipe the frosting onto each cupcake in a swirl pattern and top with a lemon wedge (if desired).


Tools You Will Need:

  • muffin or cupcake tin and liners
  • large mixing bowls
  • frosting bag and tip (or zip top bag with corner removed)

Nutrition Information:



Serving Size:


Amount Per Serving: Calories: 1709Total Fat: 13gSaturated Fat: 8gTrans Fat: 0gUnsaturated Fat: 4gCholesterol: 57mgSodium: 315mgCarbohydrates: 404gFiber: 0gSugar: 387gProtein: 4g

All nutrition information is estimated. For accuracy, please calculate your exact brands and ingredients if accuracy is desired.

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