Lemon Cupcakes

These lemon cupcakes are made using my favorite vanilla cupcake base infused with lemon zest. They’re frosted with a silky lemon cream cheese frosting and dusting of lemon zest.

Lemon is one of my favorite flavors to bake with. I have so many lemon dessert recipes and to be honest, I tested lemon cupcakes several times over the last few years and had some struggles in the past. Adding lemon juice to baked goods significantly lowers the pH, which results in a weak structure and honestly, barely adds any flavor so it can be difficult to get a good lemon cupcake/cake. 

I wanted to keep my cupcakes as close to my original vanilla cupcakes as possible (because I love them) but with a lemon flavor. After making my orange cupcakes and cranberry cupcakes I realized that the most flavor I’m going to get is by rubbing the lemon zest in with the sugar to release the oils from the lemon peel.

Why you’ll love these lemon cupcakes

  • The lemon cupcakes are simple, subtle and soooo moist.
  • The combination of the lemon cupcakes pair perfectly with the silky cream cheese frosting. 
  • Recipe is versatile – can be made with dairy free and gluten-free ingredients. 

As I mentioned, I have sooo many lemon recipes. Some of my favorites are my lemon curd cake, lemon macarons, brown butter lemon cinnamon rolls, lemon white chocolate cookies and brown butter lemon ice cream

I was really tempted to fill these or top these with lemon curd but I realized that I usually over complicate recipes and I wanted these to be simple and easy.

So I skipped it this time…but Lemon Meringue Cupcakes are on my bucket-list and you better bet they’ll be filled with lemon curd and topped with a gorgeous toasted meringue.

Ingredients & Substitutions

  • Butter: I prefer salted butter for the cupcakes and unsalted for the buttercream. You can also use unsalted butter for all of it, just add an extra pinch of salt. Make sure it’s softened to room temperature for all parts of the recipe. 
  • Flour: I use all purpose flour in most of my recipes BUT you cannot beat the texture of cake flour in cupcakes so I highly recommend King Arthur’s Cake Flour. It is far superior to some alternatives in the grocery stores.
    • I have used the “homemade cake flour” trick by replacing 1 tablespoon of all-purpose flour with cornstarch. The cupcakes will work if you make them this way but they won’t be quite as soft and tender. 
    • I HIGHLY recommend using a digital scale, as flour is so often over measured. 
  • Baking Powder: to leaven the cupcakes. 
  • Sugar: I used granulated sugar in the cupcake and I don’t recommend cutting any out.
    • I use powdered sugar in the cream cheese frosting – you can use less if you want it less sweet.
  • Lemon: I used the zest of two large lemons (or three small) for the cupcakes and a little bit of the juice in the cream cheese frosting. 
  • Oil: I always use a combination of butter and oil in my cakes because I like the texture from both. I recommend a neutral oil like vegetable oil, canola oil or sunflower oil here. 
  • Eggs: I just use one large egg and make sure it’s at room temperature. Place it in hot water for 5-10 minutes if it’s cold.
  • Sour Cream: I’ve used greek yogurt and sour cream in this recipe and they both work well. You can also use plain yogurt, just make sure it’s unsweetened.
    • However, if you sub the sour cream for extra milk, the cupcakes might shrivel up a little when cooling so I don’t recommend that.
  • Milk: I use whole milk or two percent but any milk will work here, even dairy free. 
  • Vanilla: I just use vanilla extract in this recipe but vanilla bean paste also works.
  • Cream Cheese: I always use full-fat Philadelphia cream cheese. Make sure it comes to room temperature before mixing it with the butter. 
  • Vanilla: I use pure vanilla extract in the cupcakes and vanilla bean paste in the cream cheese frosting. Either works in both though. 

Step-by-Step Instructions

Lemon Cupcakes

Step 1: Zest the lemon on top of the sugar and use your fingers to rub them together well, until they’re well combined. 

Step 2: Whisk together the flour, sugar, baking powder and salt until they’re evenly distributed.

Step 3: Add the room temperature butter and the oil and use an electric mixer to beat them at medium, until they’re crumbly like a streusel. 

Step 4: Add the egg and mix just until it’s well combined and the batter looks like paste.

Step 5: Add the sour cream and turn the mixer to low speed while streaming in the milk .

Step 6: Scrape the edge of the bowl and give it a good mix. Fill the cupcake liners about ⅔-¾ full. I recommend weighing them so each cupcake has 50-55 grams of batter.  

Step 7: Bake for 20ish minutes, until the tallest part of the cupcake, in the center, springs back when you press on it. If you’re hesitant, give it another minute or so.

Step 8: Let the cupcakes rest for 10 minutes in the pan, then remove them from the pan. 

Cream Cheese Frosting 

Step 1: Make the frosting by creaming the butter and cream cheese together until they’re well combined and have lightened in color a bit. 

Step 2: Add the powdered sugar and salt and beat at a low speed just until the sugar is combined. 

Step 3: Scrape the edge of the bowl, add the vanilla and increase the speed to medium for 1-2 minutes while streaming in the heavy whipping cream.

Step 4: If the frosting is soft, just refrigerate it for 20-30 minutes before piping. Meanwhile, use a knife or cupcake corer to cut a hole in the center of the cupcakes. 

Step 5: Frost the cupcakes with the cream cheese frosting and then top with a dusting of lemon zest.

Expert tips on getting perfect cupcakes

There’s a few things that can make it or break it with these cupcakes. 

  • Don’t swap ingredients unless I mentioned them in the ingredient section above.
  • Don’t reduce the sugar. I know a lot of people do that for some recipes but not these cupcakes. Sugar can be reduced in the powdered sugar.
  • Weigh your ingredients with a digital scale.
  • Weigh the batter for each cupcake with a digital scale. I just place the cupcake pan on the scale with the liners and measure out 50-55 grams for each cupcake, if it’s more they will likely sink/shrivel after baking.  
  • If you get each one at 50g, you may get 14 cupcakes out of the batter but if someone of them 55g of batter per cupcake, you’ll likely get 13 cupcakes with a little bit of batter left over – don’t distribute the little bit left, just toss it…or make a couple of mini cupcakes lol. 
  • Use a light colored stainless steel muffin tin for even baking. 

Frequently Asked Questions

Can I use all-purpose flour?

I have used the “homemade cake flour” trick by replacing 1 tablespoon of all-purpose flour with cornstarch. The cupcakes will work if you make them this way but they won’t be quite as soft and tender. 
I HIGHLY recommend using a digital scale, as flour is so often over measured. 

Can I make this ahead of time?

These cupcakes hold on to moisture fine so you can make it 1-2 days in advance before serving and store in an airtight container at room temperature if they’re unfrosted; refrigerated if they are frosted. Or you could make it more in advance and freeze. See the storing section. 

What if I only have one pan?

If you only have one muffin pan, the batter for the 13th cupcake can just wait on the counter until the first 12 are done baking. 

How do I know when it’s done baking?

Just like all the rest of my cakes, I test if it’s done baking by pressing gently on the tallest part of the cake. The cake will spring back if it’s done baking. If it stays indented, give it a few minutes in the oven, before testing again. 

Can I frost these with a different buttercream? 

You definitely could. You could use American buttercream or Swiss meringue buttercream or any buttercream really but I think the flavor of cream cheese pairs best with the lemon. 

Can I use this as a cake recipe?

I have not tested this cupcake recipe as a cake recipe but I don’t imagine it would be bad. It would probably make about 1 layer 8 or 9 inch cake. 
You could also use my 4 inch, 6 inch, 8 inch or 10 inch vanilla cakes and just rub the sugar with the lemon zest and add the cinnamon to get the same flavor. One batch of this frosting is enough to lightly frost a 6 inch cake. 

How to store lemon cupcakes

Anything made with cream cheese frosting needs to be stored in the refrigerator. Keep them in an airtight container in the fridge for 4-5 days or freeze for longer.

To freeze the cupcakes, place them in an airtight container and then place the container in a freezer bag, squeezing out all the excess air. Bring them back to room temperature by thawing at room temperature for a few hours before serving. 

Thanks so much for reading today’s post, if you have any questions just comment down below. 

If you make these lemon cupcakes, I’d love it if you left me a review or a star rating. 🙂

As always, have a blessed day and happy baking!

Love, B

lemon cupcakes frosted with cream cheese frosting

Lemon Cupcakes

Bernice Baran
Super moist and tender lemon cupcakes frosted with a silky lemon cream cheese frosting!
4.86 from 14 votes
Prep Time 45 minutes
Cook Time 18 minutes
Additional Time 30 minutes
Total Time 1 hour 33 minutes
Course Cupcakes
Cuisine American
Servings 14 cupcakes
Calories 417 kcal


Lemon Cupcakes

  • 1 cup (200g) granulated sugar
  • 2 large lemon (or 3 small), zested
  • 1 1/2 cup (172g) cake flour spooned and leveled
  • 1 1/2 tsp baking powder
  • 1/4 tsp fine sea salt
  • 1/4 cup (60mL) canola oil
  • 1/4 cup (56g) unsalted butter room temperature
  • 1 large egg room temperature (or 2 large egg whites if you want whiter cupcakes)
  • 1 tsp pure vanilla extract
  • 1/2 cup (113g) sour cream
  • 1/3 cup (80mL) whole milk room temperature

Cream Cheese Frosting

  • 1/2 cup (113g) unsalted butter room temperature
  • 8 oz (1 brick) cream cheese room temperature
  • 4 cups (480g) powdered sugar spooned and leveled
  • tiny pinch fine sea salt
  • 2-3 Tbsp (30-45mL) lemon juice room temperature
  • 2 tsp vanilla bean paste (or vanilla extract)


Lemon Cupcakes

  • Preheat the oven to 350F/177C convection (325F/163C conventional) and line 13-14 muffin tins with cupcake liners (preferably a light colored pan).
  • Place the sugar in the bowl of a stand mixer (or a large bowl) and zest the lemon on top. Use your fingers to rub the sugar with the lemon zest to release the oils.
    1 cup (200g) granulated sugar, 2 large lemon (or 3 small), zested
  • Add the cake flour, baking powder and salt and whisk until they're evenly distributed.
    1 1/2 cup (172g) cake flour, 1 1/2 tsp baking powder, 1/4 tsp fine sea salt
  • Add the oil and butter to the dry ingredients and beat together until they're combined.
    1/4 cup (60mL) canola oil, 1/4 cup (56g) unsalted butter
  • Add the egg and vanilla extract and mix until they're fully combined.
    1 large egg, 1 tsp pure vanilla extract
  • Add the sour cream and turn the mixer to low speed, while streaming the milk in. Scrape the edge of the bowl and mix just until the cupcake batter is smooth.
    1/2 cup (113g) sour cream, 1/3 cup (80mL) whole milk
  • Fill each cupcake liner about 2/3-3/4 full, about 50-55 grams of batter per cupcake.* You will have enough batter for about half a cupcake leftover. DO NOT BE TEMPTED to distribute that among the cupcakes, they will sink if they’re overfilled.
  • Bake for 16-18 minutes. They are done when you press on the center of the cupcake and it springs back or when a toothpick inserted comes out clean.
  • Remove them from the oven and let them cool in the cupcake pan for 10 minutes, then move them to a cooling rack. Allow the cupcakes to cool completely before frosting.

Cream Cheese Frosting

  • Place the room temperature butter in the bowl of a stand mixer. Using a whisk attachment, beat the butter on medium-high speed for 1-2 minutes, until the color turns to a pale yellow.
    1/2 cup (113g) unsalted butter
  • Add in the cream cheese and beat at medium speed for a minute, just until they're combined
    8 oz (1 brick) cream cheese
  • Add the powdered sugar and salt and mix on low speed, just until it's combined. Turn the mixer to medium-high speed and beat the buttercream for 2-3 minutes, until all of the sugar is fully dissolved and the buttercream no longer feels gritty. 
    4 cups (480g) powdered sugar, tiny pinch fine sea salt
  • Pour in the 2-3 tablespoons of lemon juice and vanilla bean paste and beat for another 1-2 minutes on high speed. 
    2-3 Tbsp (30-45mL) lemon juice, 2 tsp vanilla bean paste
  • If the frosting is too soft, refrigerate it for 20-30 minutes. Use a piping bag fit a large round tip to pipe the cream cheese frosting on top of the cupcakes. Top with a little lemon zest of lemon peels.


  • *I weigh 55g of batter for each cupcake. If it’s less, they’ll be short and if it’s too much, they may sink.
  • If you get each one at 50g, you may get 14 cupcakes out of the batter but if someone of them 55g of batter per cupcake, you’ll likely get 13 cupcakes with a little bit of batter left over – don’t distribute the little bit left, just toss it…or make a couple of mini cupcakes lol. 
  • I recommend a light colored metal cupcake pan if you want them more uniform in color.
  • Store in an airtight container, refrigerated for 4-5 days or frozen for a few weeks.


Serving: 1gCalories: 417kcalCarbohydrates: 53gProtein: 3gFat: 22gSaturated Fat: 11gPolyunsaturated Fat: 2gMonounsaturated Fat: 7gTrans Fat: 0.4gCholesterol: 60mgSodium: 149mgPotassium: 65mgFiber: 0.3gSugar: 42gVitamin A: 599IUVitamin C: 1mgCalcium: 64mgIron: 0.3mg
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