Simple Lemon Cupcakes with Cream Cheese Icing

I was in my twenties before I realized that lemon cupcakes didn’t have to come from a box mix. My mom always grabbed the yellow cake mix from the grocery store and called it good. When I tried making them from scratch the first time, they turned out flat and sad.

That’s because I was overthinking it—I was measuring everything too precisely and overmixing the batter. Fresh lemon cupcakes, on the other hand, just need real lemon juice, a gentle hand, and that tangy cream cheese frosting on top. For anyone who’s tired of artificial lemon flavor, these are a game-changer.

What Kind of Lemons Should I Use?

For the best lemon cupcakes, you’ll want to use fresh lemons rather than bottled lemon juice – the difference in flavor is really noticeable. Meyer lemons are a great choice if you can find them since they’re sweeter and less acidic than regular lemons, but standard grocery store lemons work perfectly fine too. When picking out lemons, look for ones that feel heavy for their size and have smooth, bright yellow skin – these will give you the most juice and the best zest. Make sure to wash and dry your lemons well before zesting, and try to only zest the yellow part of the peel since the white pith underneath can be bitter.

Options for Substitutions

These lemon cupcakes are pretty forgiving when it comes to swaps, so here are some options if you’re missing ingredients:

• Lemon extract: If you don’t have lemon extract, you can use vanilla extract instead, though you’ll lose some of that bright lemon flavor. For a stronger lemon taste, add an extra tablespoon of lemon juice to the batter.
• Fresh lemon juice and zest: Bottled lemon juice works in a pinch, but fresh really makes a difference here. If you only have bottled, use the same amount but maybe add a tiny bit of lemon extract to boost the flavor.
• Milk: Buttermilk, almond milk, or even water will work as substitutes. Buttermilk will give you extra tang, while non-dairy milk keeps the texture similar.
• Cream cheese: You can make a simple buttercream instead by using all butter (about 1 cup total) and following the same mixing method. The flavor will be different but still tasty.
• Unsalted butter: Salted butter works fine – just reduce the kosher salt in the cupcake batter to ¼ teaspoon to balance things out.
• All-purpose flour: Cake flour will give you lighter cupcakes – use 1 ⅔ cups instead of 1 ½ cups all-purpose flour.

Watch Out for These Mistakes While Baking

The biggest mistake when making lemon cupcakes is not having your butter, eggs, and cream cheese at proper room temperature – cold ingredients won’t cream together properly and can lead to dense, lumpy cupcakes and grainy frosting.

Another common error is overmixing the batter once you add the flour, which develops too much gluten and creates tough, chewy cupcakes instead of light and fluffy ones – mix just until the ingredients are combined.

Don’t skip sifting your powdered sugar for the frosting, as lumps will make your icing look unprofessional, and be sure to zest your lemons before juicing them since it’s much easier to work with whole fruit.

Finally, resist the urge to frost warm cupcakes, as the heat will melt your cream cheese frosting and turn it into a drippy mess – let them cool completely on a wire rack first.

What to Serve With Lemon Cupcakes?

These lemon cupcakes are perfect on their own, but they really shine when served alongside fresh berries like strawberries or blueberries that complement the citrus flavors. A cup of hot tea or coffee makes a great pairing, especially Earl Grey or a light roast that won’t compete with the bright lemon taste. For special occasions, try serving them with a scoop of vanilla ice cream or a dollop of whipped cream for an extra indulgent treat. They’re also wonderful as part of a dessert spread with other light, fruity treats like shortbread cookies or fruit tarts.

Storage Instructions

Keep Fresh: These lemon cupcakes with cream cheese icing need to be stored in the refrigerator because of the cream cheese frosting. Pop them in an airtight container and they’ll stay fresh for up to 5 days. Just let them sit at room temperature for about 15 minutes before serving so the frosting softens up nicely.

Freeze: You can freeze these cupcakes for up to 3 months! I like to freeze them unfrosted first, then add the cream cheese icing after they thaw. If you want to freeze them already frosted, place them on a baking sheet until the frosting hardens, then transfer to a freezer container.

Make Ahead: The cupcakes themselves can be baked a day or two ahead and stored covered at room temperature before frosting. You can also make the cream cheese icing up to 3 days in advance and keep it in the fridge – just give it a good stir before using since it might separate slightly.

Estimated Nutrition

Estimated nutrition for the whole recipe (without optional ingredients):

• Calories: 4000-4300
• Protein: 32-38 g
• Fat: 165-180 g
• Carbohydrates: 610-650 g

Ingredients

For the cupcakes:

• 1 stick unsalted butter, at room temperature
• 1 cup white sugar
• 2 large eggs
• 2 tsp lemon extract
• 1 1/2 cups all-purpose flour, unbleached
• 2 tsp baking powder
• 1/2 tsp kosher salt
• 1/2 cup milk
• Zest from 1 medium lemon
• 1/4 cup lemon juice (from 1 medium lemon)

For the cream cheese icing:

• 8 oz cream cheese, room temperature
• 4 tbsp unsalted butter, room temperature
• 1 lb sifted confectioners’ sugar
• Zest of 1 medium lemon
• 1 tsp vanilla extract

Step 1: Prepare the Lemon Cupcake Batter

• 1 stick unsalted butter, at room temperature
• 1 cup white sugar
• 2 large eggs
• 2 tsp lemon extract
• 1 1/2 cups all-purpose flour, unbleached
• 2 tsp baking powder
• 1/2 tsp kosher salt
• 1/2 cup milk
• zest from 1 medium lemon
• 1/4 cup lemon juice (from 1 medium lemon)

Preheat your oven to 350°F.

In a large bowl, beat the room temperature unsalted butter and white sugar together until the mixture is pale and fluffy.

Add the eggs one at a time, fully incorporating each before adding the next, followed by the lemon extract.

In a separate bowl, whisk together the all-purpose flour, baking powder, and kosher salt.

Alternate adding the dry ingredients and milk to the butter mixture, starting and finishing with the flour mix.

Gently fold in the lemon zest and lemon juice at the end to give the batter a fragrant citrus lift.

Step 2: Bake the Cupcakes

Line a 12-cupcake pan (or 6 large cupcake pan) with muffin liners.

Divide the prepared batter evenly, filling each liner about two-thirds full.

Place the pan in the preheated oven and bake for 18-20 minutes, or until the cupcakes are lightly golden and a toothpick inserted comes out clean.

Remove from the oven and let them cool completely in the pan before frosting.

I like to let the cupcakes cool fully so the icing doesn’t melt—patience pays off for perfect results!

Step 3: Prepare the Lemon Cream Cheese Frosting

• 8 oz cream cheese, room temperature
• 4 tbsp unsalted butter, room temperature
• 1 lb sifted confectioners’ sugar
• zest of 1 medium lemon
• 1 tsp vanilla extract

While the cupcakes are baking, make the frosting.

In a large bowl, beat the room temperature cream cheese and unsalted butter together with a hand mixer on medium speed until light and fluffy, about 1 minute.

Add the sifted confectioners’ sugar, lemon zest, and vanilla extract gradually.

Continue beating until the frosting is smooth and fluffy, perfect for spreading or piping.

For a more pronounced lemony taste, I sometimes sneak in an extra pinch of zest here!

Step 4: Frost and Serve the Cupcakes

Once the cupcakes are completely cool, generously ice them with the lemon cream cheese frosting from Step 3.

Use a spatula or piping bag as you prefer.

These cupcakes are at their best within three days of baking, so enjoy them fresh for maximum flavor.

Simple Lemon Cupcakes with Cream Cheese Icing

Delicious Simple Lemon Cupcakes with Cream Cheese Icing recipe with step-by-step instructions.

Print Recipe Pin Recipe

Prep Time 13 minutes mins

Cook Time 26 minutes mins

Total Time 39 minutes mins

Servings 4

Calories 4150 kcal

Ingredients

  

For the cupcakes:

• 1 stick unsalted butter, at room temperature
• 1 cup white sugar
• 2 large eggs
• 2 tsp lemon extract
• 1 1/2 cups all-purpose flour, unbleached
• 2 tsp baking powder
• 1/2 tsp kosher salt
• 1/2 cup milk
• zest from 1 medium lemon
• 1/4 cup lemon juice (from 1 medium lemon)

For the cream cheese icing:

• 8 oz cream cheese, room temperature
• 4 tbsp unsalted butter, room temperature
• 1 lb sifted confectioners' sugar
• zest of 1 medium lemon
• 1 tsp vanilla extract

Instructions

 

• Preheat your oven to 350°F. In a large bowl, beat the room temperature unsalted butter and white sugar together until the mixture is pale and fluffy. Add the eggs one at a time, fully incorporating each before adding the next, followed by the lemon extract. In a separate bowl, whisk together the all-purpose flour, baking powder, and kosher salt. Alternate adding the dry ingredients and milk to the butter mixture, starting and finishing with the flour mix. Gently fold in the lemon zest and lemon juice at the end to give the batter a fragrant citrus lift.
• Line a 12-cupcake pan (or 6 large cupcake pan) with muffin liners. Divide the prepared batter evenly, filling each liner about two-thirds full. Place the pan in the preheated oven and bake for 18-20 minutes, or until the cupcakes are lightly golden and a toothpick inserted comes out clean. Remove from the oven and let them cool completely in the pan before frosting. I like to let the cupcakes cool fully so the icing doesn’t melt—patience pays off for perfect results!
• While the cupcakes are baking, make the frosting. In a large bowl, beat the room temperature cream cheese and unsalted butter together with a hand mixer on medium speed until light and fluffy, about 1 minute. Add the sifted confectioners' sugar, lemon zest, and vanilla extract gradually. Continue beating until the frosting is smooth and fluffy, perfect for spreading or piping. For a more pronounced lemony taste, I sometimes sneak in an extra pinch of zest here!
• Once the cupcakes are completely cool, generously ice them with the lemon cream cheese frosting from Step 3. Use a spatula or piping bag as you prefer. These cupcakes are at their best within three days of baking, so enjoy them fresh for maximum flavor.