Indulge in Zesty Perfection: The Ultimate Lemon Bar Cupcakes
Prepare to delight your taste buds with these extraordinary Lemon Bar Cupcakes! Imagine super moist, vibrant lemon cupcakes, each lovingly filled with a luscious, tangy lemon bar filling, and crowned with a swirl of dreamy lemon cream cheese frosting. To top it all off, a final flourish of that irresistible lemon bar filling creates a visual masterpiece and an explosion of citrus flavor in every bite. These aren’t just any cupcakes; they are a celebration of intense lemon flavor and a perfect symphony of textures, offering just the right balance of sweet and tart that lemon lovers crave.
Our recipe elevates the classic lemon bar experience, transforming it into a convenient, delightful cupcake form. We achieve this profound lemon flavor by incorporating fresh lemon zest and generous amounts of fresh lemon juice into every component – the cake, the filling, and the frosting. For that perfect hint of sweetness and an added layer of richness, we’ve also included premium honey, creating a dessert that’s both comforting and sophisticated.
This post is proudly sponsored by Wholesome, a brand committed to high-quality, organic sweeteners. All thoughts and opinions expressed here are genuinely my own. Your support for brands like Wholesome makes it possible for Stephanie’s Sweet Treats to continue sharing delightful recipes with you!
I have received compensation from Wholesome Sweeteners, Inc., the esteemed maker of Wholesome® sweeteners, for my participation in this promotional campaign.

These lemon bar cupcakes are not merely a dessert; they are an experience tailored for anyone who truly appreciates the bright, invigorating taste of lemon. By capturing the powerful and distinct flavors of traditional lemon bars and reimagining them in a moist, tender cupcake, we’ve crafted an easy-to-make treat that is sure to win over even the most discerning lemon dessert enthusiasts. Their perfect balance of sweetness, accentuated by a delightful tartness, makes them an unforgettable indulgence for any occasion.
Central to the exquisite flavor profile of these cupcakes is the use of Wholesome Organic Fair Trade Raw and Unfiltered Honey. I consistently choose Wholesome for my baking endeavors because of their unwavering commitment to high-quality honey and other sweeteners. Their organic, fair trade raw and unfiltered honey is sustainably harvested by dedicated beekeepers in certified organic zones deep within the lush forests of South America, ensuring both purity and ethical sourcing. This dedication to quality shines through in every bite of these delightful cupcakes.
If you’re looking to explore more delicious cupcake creations, be sure to try our other popular recipes, including Biscoff Cupcakes, S’mores Cupcakes, and Strawberry Filled Cupcakes.
Why These Lemon Bar Cupcakes Will Be Your New Favorite
This recipe isn’t just another dessert; it’s a carefully crafted creation designed to deliver an unparalleled lemon experience. Here’s why these lemon bar cupcakes stand out:
- Triple Lemon Flavor Explosion: We’ve infused lemon into every single layer of these cupcakes – the tender cake base, the rich filling, and the velvety cream cheese frosting. This multi-layered approach ensures a consistently strong, bright, and delightful lemon flavor that permeates every mouthful. It’s a true celebration of citrus!
- Unbelievably Moist and Tender Cupcakes: Say goodbye to dry, crumbly cupcakes! Our secret combination of ingredients, including sour cream and buttermilk, guarantees a super moist and incredibly tender crumb. The texture is so perfect, it feels like you’re biting into a cloud – a hallmark of the very best homemade baked goods.
- Irresistible Homemade Lemon Bar Filling: The heart of these cupcakes is a homemade lemon bar filling that is pure bliss. This creamy, tangy, and sweet lemon curd-like filling takes these cupcakes to an entirely new level, adding a luxurious burst of flavor and a delightful textural contrast that makes them truly exceptional.
- Surprisingly Simple to Make: Don’t let the “filled cupcake” title intimidate you. While filled cupcakes might seem complex, this lemon cupcake recipe is designed with simplicity in mind. We’ve broken down each component and step into easy-to-follow instructions, ensuring even novice bakers can achieve spectacular results with confidence.

Essential Ingredient Notes for Perfect Lemon Bar Cupcakes
Success in baking often hinges on understanding your ingredients. Here are some detailed notes on the key components for these lemon bar cupcakes. For the complete list of quantities, please refer to the comprehensive recipe card below.
- Wholesome Organic Fair Trade Raw and Unfiltered Honey: This isn’t just any honey! Being raw and unfiltered means it retains some of its natural pollen, enzymes, and beneficial nutrients, contributing a more complex, nuanced sweetness and a delicate floral note to your cupcakes. Its fair trade certification also means you’re supporting ethical sourcing.
- Unsalted Butter: Always opt for unsalted butter to control the overall salt content in your recipe. It’s crucial that your butter is at **room temperature** – ideally, pull it out of the fridge at least 2 hours before you plan to bake. Room temperature butter creams better with sugar, incorporating air for a light and fluffy cake texture.
- Sour Cream: For maximum moistness and a tender crumb, use full-fat sour cream. If sour cream isn’t available, full-fat plain Greek yogurt makes an excellent substitute, offering similar moisture and a slight tang. Like butter, ensure it’s at **room temperature** for optimal blending.
- Large Eggs: Large eggs are the standard for most baking recipes. Just like the butter and sour cream, bring your eggs to **room temperature** before mixing. Room temperature eggs emulsify better with other ingredients, creating a smoother, more uniform batter and a better-textured cupcake.
- Oil (Canola or Vegetable): A touch of neutral-flavored oil, such as canola or vegetable oil, contributes to the cupcakes’ moistness and helps keep them tender for longer, preventing them from drying out quickly.
- Sugar: We recommend Wholesome Organic Fair Trade Cane Sugar for its consistent quality and clean sweetness. This granular sugar not only sweetens but also aids in aeration when creamed with butter.
- Buttermilk: Full-fat or reduced-fat buttermilk works wonderfully here. The acidity in buttermilk reacts with the baking soda, creating a lighter, more tender crumb. It also helps to activate the lemon flavor. Ensure your buttermilk is at **room temperature** before using.
- Powdered Sugar (Confectioners Sugar): For the smoothest, silkiest frosting, Wholesome Organic Fair Trade Powdered Confectioners Sugar is an excellent choice. It is absolutely essential to **sift** your powdered sugar before adding it to the frosting to eliminate any lumps and ensure a perfectly smooth, creamy texture.
- Fresh Lemons: The star of the show! Use medium-sized fresh lemons for both zest and juice. The zest carries the most potent lemon oil, providing intense flavor without adding too much acidity. Always zest your lemons *before* juicing them; it’s much easier! Freshly squeezed lemon juice is paramount for the bright, tangy flavor that defines these cupcakes and their filling.
Step-By-Step Instructions: Crafting the Silky Lemon Bar Filling
Creating this irresistible lemon bar filling is the first crucial step to ensure it has ample time to cool and set, which is essential for a perfectly textured filling. Follow these simple steps for a lusciously smooth result:
STEP 1: Combine Ingredients. In a sturdy medium saucepan, whisk together the organic cane sugar, rich egg yolks, cornstarch (which acts as a thickening agent), vibrant lemon zest, fresh lemon juice, pure vanilla extract, a pinch of salt, and the raw unfiltered honey. Whisk vigorously until all ingredients are thoroughly combined and no lumps remain.
STEP 2: Cook to Perfection. Place the saucepan on your stove over medium-low heat. Using a heat-resistant rubber spatula, stir the mixture continuously. This constant stirring is key to preventing the eggs from scrambling and ensuring even cooking. Continue stirring until the mixture visibly thickens and reaches a temperature of 170°F (77°C) on a reliable instant-read thermometer. This process typically takes about 2-3 minutes, but keep a close eye on it, as precise temperature control ensures the filling sets correctly.
STEP 3: Incorporate Butter for Richness. Immediately remove the pan from the heat. While the filling is still hot, add the cubed unsalted butter. Stir well with your rubber spatula until the butter has completely melted into the lemon mixture and is fully incorporated, creating a smooth, glossy, and enriched filling.
STEP 4: Cool and Chill. Pour the warm lemon filling into a clean bowl. To prevent a skin or film from forming on the surface as it cools, press a piece of plastic wrap directly onto the surface of the filling. Place the bowl in the refrigerator and allow it to cool completely. This cooling process is vital for the filling to achieve its thick, spreadable consistency, perfect for piping into your cupcakes.


Step-By-Step Instructions: Baking Flawless Lemon Cupcakes
Now, let’s turn our attention to crafting the perfectly moist and tender lemon cupcakes. This recipe greatly benefits from the use of an electric mixer. I personally use a stand mixer with a paddle attachment for ease, but a good quality hand mixer will also work, though it might require a bit more effort for beating the butter mixture.
STEP 1: Prepare Your Workspace. Begin by preheating your oven to 350°F (175°C). Next, take a standard 12-cup muffin tin and line each cavity with paper muffin liners. This ensures your cupcakes bake evenly and are easy to remove.
STEP 2: Whisk Dry Ingredients. In a medium-sized bowl, sift together the all-purpose flour, baking powder, baking soda, and salt. Sifting is an important step as it removes any lumps, aerates the flour, and ensures all dry ingredients are evenly distributed, contributing to a finer, more consistent cake crumb. Set this bowl aside.
STEP 3: Cream Butter and Sugars. In the bowl of your electric mixer (or a large mixing bowl if using a hand mixer), combine the softened unsalted butter, neutral oil, raw honey, and organic cane sugar. Beat this mixture on high speed for a full 3 minutes. It’s crucial not to rush this step; proper creaming incorporates air, making the mixture light, fluffy, and pale in color, which is essential for a soft, tender cupcake.
STEP 4: Incorporate Wet Ingredients. Reduce the mixer speed to low. Add the fresh lemon zest, fresh lemon juice, room temperature sour cream, and large eggs to the creamed butter and sugar mixture. Mix until just combined. You might notice that the batter appears slightly separated or curdled due to the acidity of the lemon reacting with the dairy. This is completely normal and does not indicate a problem with your batter.
STEP 5: Alternate Dry and Wet. With the mixer still on low speed, gradually add the dry ingredients and buttermilk in alternating batches. Begin by adding about one-third of the dry ingredient mixture, mixing until just combined. Then, add half of the buttermilk and mix until just incorporated. Repeat this process with the second third of the dry ingredients and the remaining buttermilk. Finally, add the last third of the dry ingredients and mix only until no streaks of flour are visible. Be careful not to overmix the batter, as this can lead to tough cupcakes.
STEP 6: Fill Cupcake Liners. Using a cookie scoop (a standard 2-tablespoon scoop works well for this), fill each prepared muffin liner approximately two-thirds full. It’s important not to overfill the liners, as this can cause the cupcakes to overflow and bake unevenly, resulting in dense centers or domed tops.


STEP 7: Bake Until Golden. Transfer the muffin tin to your preheated oven and bake for 16-18 minutes. Cupcakes are fully baked when a toothpick inserted into the center of one comes out clean or with only a few moist crumbs attached. The tops should be lightly golden and spring back when gently touched.
STEP 8: Cool Completely. Once baked, remove the muffin tin from the oven. Allow the cupcakes to cool in the pan for about 10 minutes. This allows them to firm up slightly before you transfer them to a wire rack to cool completely. Cooling on a wire rack is crucial to prevent the bottoms from becoming soggy and to ensure they are fully cooled before frosting.


Step-By-Step Instructions: Whipping Up Lemon Cream Cheese Frosting & Assembly
The final touches bring these lemon bar cupcakes to life! Here’s how to create the luscious lemon cream cheese frosting and assemble your magnificent treats.
STEP 1: Sift Powdered Sugar. First, sift the powdered sugar into a medium bowl. This crucial step prevents lumps and ensures your frosting will be wonderfully smooth and creamy. Set aside.
STEP 2: Cream Butter and Cream Cheese. In the bowl of your electric mixer, combine the room temperature unsalted butter and softened cream cheese. Beat on high speed for 2 minutes until the mixture is incredibly light, fluffy, and completely smooth. Scrape down the sides of the bowl often to ensure everything is evenly incorporated.
STEP 3: Blend in Remaining Ingredients. Gradually add half of the sifted powdered sugar to the butter and cream cheese mixture. Mix on low speed until it’s just combined. Then, add the remaining half of the powdered sugar and continue mixing on low until fully incorporated. Once the sugar is in, add the fresh lemon zest and a pinch of salt. Increase the mixer speed to high and beat for another 1-2 minutes until the frosting is exceptionally creamy, smooth, and fluffy. The lemon zest will infuse the frosting with a bright, aromatic lemon flavor.

STEP 4: Core the Cupcakes. Once your cupcakes are completely cool, it’s time to prepare them for filling. Use a cupcake corer to create a hole in the center of each cupcake, going approximately halfway down. If you don’t have a corer, a small, sharp knife or the back of a spoon can work just as well. Gently remove the cored centers and set them aside (you can save these for a fun cake pop experiment later, or discard them).
STEP 5: Fill with Lemon Goodness. Take your chilled lemon bar filling. Using a ½ tablespoon scoop or a small spoon, carefully fill each cored cupcake with a generous dollop of the rich lemon bar filling. Ensure the filling reaches the bottom of the hole for a burst of flavor in every bite.
STEP 6: Frost Generously. Now for the frosting! Use a large cookie scoop to portion a generous amount of lemon cream cheese frosting onto the top of each filled cupcake. Then, using an offset spatula or the back of a spoon, gently spread and swirl the frosting evenly over the top of the cupcake, creating a beautiful domed effect.
STEP 7: Swirl in Extra Flair. For an elegant finishing touch and an extra burst of lemon, place about 1 teaspoon of the reserved lemon bar filling directly in the center of the frosted cupcake. Then, use the tip of a spoon or a toothpick to gently drag it through the frosting, creating a beautiful swirl design that hints at the delicious filling within.


Expert Baking Tips for Flawless Lemon Bar Cupcakes
Achieving bakery-quality cupcakes at home is entirely possible with a few professional insights. Here are some expert baking tips to ensure your lemon bar cupcakes turn out perfectly every time:
- Measure Flour Correctly: This is one of the most common baking mistakes! Always “spoon and level” your flour. Instead of scooping your measuring cup directly into the flour bag (which compacts it), gently spoon the flour into the measuring cup until it overflows, then level it off with the back of a knife. Alternatively, for ultimate precision, use a kitchen scale to measure flour by weight (1 cup all-purpose flour typically weighs around 120-125 grams). Compacted flour results in too much flour, leading to dry, dense cupcakes.
- Cream Butter and Sugar Thoroughly: The step where you beat the butter, oil, honey, and sugar for 3 minutes is vital for aerating the mixture. This process incorporates tiny air pockets, which expand during baking, contributing to a light, soft, and tender cupcake texture. If this step is rushed or not done sufficiently, your cupcakes may be denser and less delicate.
- Room Temperature Ingredients are Non-Negotiable: We cannot stress this enough! Ensuring your butter, eggs, sour cream, and buttermilk are all at room temperature is crucial. Room temperature ingredients emulsify more effectively, creating a smooth, uniform batter that traps air better and bakes more evenly. This results in a superior texture and consistency in your finished cupcakes. Plan ahead and pull them out of the refrigerator at least 1-2 hours before you begin baking.
- Don’t Overmix the Batter: Once you start adding the dry ingredients, mix only until just combined and no streaks of flour are visible. Overmixing develops the gluten in the flour, leading to tough, chewy cupcakes rather than light and tender ones. A gentle hand is key!
- Use a Reliable Oven Thermometer: Oven temperatures can vary significantly from what the dial indicates. An inexpensive oven thermometer placed inside your oven will give you an accurate reading, helping you maintain the correct baking temperature and prevent under or over-baking.
- Repurpose Cupcake Cores: Don’t waste those delicious cupcake cores! You can mix them with any leftover lemon cream cheese frosting to create delightful lemon cake balls. Simply roll them into small spheres, chill, and dip them in melted white chocolate for an extra treat.
- High-Altitude Adjustments: If you bake at a high altitude (generally 3,500 feet or 1,000 meters above sea level), you might need to make minor adjustments. A common tip is to add an extra 1 tablespoon of all-purpose flour to the cupcake batter to help stabilize it and prevent excess spreading. You may also need to slightly increase liquids or decrease baking soda/powder.

Frequently Asked Questions (FAQ) About Lemon Bar Cupcakes
Here are answers to some common questions about making and enjoying these delectable lemon bar cupcakes:
Absolutely! These cupcakes are excellent for making ahead. Once the cupcakes have fully cooled after baking, wrap them individually in plastic wrap to prevent them from drying out. You can then freeze them in an airtight container for up to 30 days. When you’re ready to enjoy them, thaw the frozen cupcakes at room temperature for about 1 hour before you proceed with filling and decorating. This makes party planning a breeze!
While these lemon cupcakes are certainly delicious even without the added lemon curd filling, we strongly encourage you to include it. The homemade lemon bar filling truly elevates these cupcakes to another level, adding an incredible burst of tangy flavor and a creamy texture that transforms them from a simple lemon cupcake into something truly extraordinary. It’s the “bar” in “lemon bar cupcake,” after all!
Yes, you can easily adapt this recipe to make adorable mini lemon bar cupcakes! The process remains largely the same, but you’ll need to adjust the baking time. For mini cupcakes, bake them for a shorter duration, typically around 8-10 minutes. Keep a close eye on them and perform the toothpick test to ensure they are baked through.
The key to a perfectly stable cream cheese frosting is using very cold cream cheese and butter that is at room temperature but still firm enough. If your frosting seems too soft, you can chill the mixing bowl (with the frosting inside) in the refrigerator for 15-20 minutes, then re-whip it until it reaches the desired consistency. Also, ensure you are sifting your powdered sugar thoroughly.
The most common reason for a thin lemon filling is not cooking it to the correct temperature or for long enough. Ensure you bring the mixture to 170°F (77°C) and stir continuously. The cornstarch is crucial for thickening, so double-check your measurements. If it’s still too thin after cooling, you can gently reheat it over low heat, stirring constantly, and add a tiny bit more cornstarch mixed with cold water to form a slurry, then cook until thickened.

Storing and Freezing Your Lemon Bar Cupcakes
To maintain their freshness and incredible flavor, proper storage is essential for your lemon bar cupcakes. Because they feature a cream cheese frosting and a lemon curd-like filling, they require refrigeration.
Store these lemon bar cupcakes in an airtight container in the refrigerator for up to 5 days. For the absolute best flavor and texture experience, allow the cupcakes to sit at room temperature for approximately 1 hour before serving. This brings the frosting and cake to a softer, more enjoyable consistency, enhancing their rich lemon notes.
Freezing Decorated Lemon Bar Cupcakes
Yes, you can freeze fully decorated lemon bar cupcakes! To do so, first place the cupcakes on a baking sheet and freeze for about 30 minutes, or until the frosting is firm. This prevents the frosting from sticking to the wrap. Then, individually wrap each cupcake tightly in plastic wrap, followed by a layer of aluminum foil. Place the wrapped cupcakes in an airtight freezer-safe container to protect them from freezer burn. They can be frozen for up to 30 days. When you’re ready to indulge, thaw the frozen cupcakes at room temperature for 1-2 hours, or overnight in the refrigerator, before serving. Enjoying them at room temperature will yield the best results.

Other Zesty Lemon Recipes to Brighten Your Day
If you’re as passionate about lemon desserts as we are, you’ll love exploring these other bright and tangy recipes:
- Lemon Poppy Seed Loaf Cake
- Lemon Meringue Pie
- Raspberry Lemonade Bars
- Blueberry Lemon Scones
We truly hope you adore these Lemon Bar Cupcakes! If you loved this recipe, please make sure to leave a STAR REVIEW below. We always love to see your creations! Tag us on Instagram @stephaniesweettreats. For more delicious inspiration and baking ideas, make sure to follow me on Pinterest. Happy baking!

Lemon Bar Cupcakes
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Ingredients
Lemon Cupcakes
- 1 3/4 cups All-purpose flour
- 1 tsp Baking powder
- 1/4 tsp Baking soda
- 1/2 tsp Salt
- 6 TBSP Unsalted butter, room temperature
- 2 TBSP Oil, canola or vegetable
- 2 TBSP Organic Fair Trade Raw and Unfiltered Honey
- 3/4 cup Wholesome Organic Fair Trade Cane Sugar
- 2 Lemons, zested
- 2 TBSP Lemon juice, 1 lemon juiced
- 1/4 cup Sour cream, room temperature
- 2 Large eggs, room temperature
- 1/2 cup Buttermilk, room temperature
Lemon Bar Filling
- 1/2 cup Wholesome Organic Fair Trade Cane Sugar
- 3 Egg yolks
- 2 Lemon zested
- 1 tsp Cornstarch
- 2 TBSP Lemon juice, juice of 1 lemon
- 1 tsp Pure vanilla extract
- 1/4 tsp Salt
- 2 TBSP Organic Fair Trade Raw and Unfiltered Honey
- 1/4 cup Unsalted butter, cubed
Lemon Cream Cheese Frosting
- 1 1/2 cups Unsalted butter, room temperature
- 16 oz Cream cheese, room temperature
- 4 cups Wholesome Organic Fair Trade Powdered Confectioners Sugar, sifted
- 2 Lemons zested
- 1/4 tsp Salt
Instructions
Lemon Bar Filling
- Start the filling first, so it can cool completely. In a medium sauce pan, add sugar, egg yolks, cornstarch, lemon zest, lemon juice, vanilla, salt, and honey. Use a whisk to mix it together.
- Place on the stove over medium-low heat. Mix using a rubber spatula. Mix until it thickens and reaches 170°F. This took me 2-3 minutes. Remove from heat and add in the cubed butter. Mix until melted and mixed together.
- Pour the filling into a bowl and place plastic wrap over the filling. This will prevent a film from forming over the top. Place in the fridge to cool completely.
Lemon Cupcakes
- Preheat the oven to 350°F. Line a 12 cup muffin tin with muffin liners.
- In a medium bowl, mix the flour, baking powder, baking soda, and salt. Set aside.
- Using a mixer, beat the butter, oil, honey, and sugar on high speed for 3 minutes. It will become light and fluffy.
- Add in the lemon zest, lemon juice, sour cream, and eggs. Mix until combined. The batter will appear separated, but it isn’t. It is just the acid from the lemon.
- Add 1/3rd of the dry ingredients and half of the buttermilk and mix on low speed. Add another 1/3rd of the dry ingredients and the rest of the buttermilk. Then, finish with the rest of the dry ingredients.
- Use a cookie scoop to scoop the dough into the muffin liners. Fill 2/3rds full. Any more, and cupcakes will over fill.
- Bake for 16-18 minutes. The cupcakes are done baking when a toothpick inserted comes out clean.
- Let the cupcakes sit in the hot pan for 10 minutes before transferring to a cooling rack. Cool completely.
Lemon Cream Cheese Frosting
- In a medium bowl, sift the powdered sugar. Set aside.
- Using a mixer, beat the butter and cream cheese on high speed for 2 minutes until creamy.
- Add in half of the powdered sugar and mix on low speed until combined. Then, add in the other half of the powdered sugar. Mix until combined. Add in lemon zest and salt and mix on high until creamy.
- Use a cupcake corer or a sharp knife to cut a hole in the middle of the cupcake about 1/2 way down. Toss the tops of the cupcakes.
- Use a 1/2 TBSP to fill the cupcakes with the lemon bar filling.
- Use a large cookie scoop to scoop the frosting on top of each cupcake. Use an offset spatula to spread the frosting on top.
- Use 1 tsp of the lemon filling and place in the middle of the cupcake. Use a spoon to drag the lemon through the frosting.
Notes
High altitude baking: Add an extra 1 TBSP of flour.
Pull out dairy ingredients 2 hours before baking.
