Lemon Poppy Seed Cupcakes

I’m a big fan of lemon poppy seed muffins, and they’re the inspiration behind these lemon poppy seed cupcakes.

After all, a muffin is really just a cupcake without frosting, right??

These lemon poppy seed cupcakes are bursting with citrus flavor! They bake up tender, soft, and absolutely delicious.

They’re topped with lemon cream cheese frosting, filled with lemon curd, and garnished with an adorable lemon peel heart.

This recipe is a summer staple in my kitchen, and I’m sure you’ll feel the same way about it!

Making These Lemon Poppy Seed Cupcakes Together

Let’s walk through each step of this lemon poppy seed cupcake recipe to make sure it turns out as amazing as possible!

I’ve also shared a video tutorial below.

Step 1: Massage the Lemon Zest into the Sugar

Add the granulated sugar and lemon zest to a large bowl. Use your fingertips to massage the zest into the sugar to help release the oil in the zest.

You should be able to smell the oils being incorporated into the sugar. This helps give these cupcakes a bright, citrusy flavor that won’t bake off in the oven. Set aside.

Step 2: Make the Lemon Poppy Seed Cupcake Batter

Next, we tackle the lemon poppy seed cupcakes! Preheat the oven to 350°F/175°C and line a muffin pan with 12 cupcake liners.

Make the cupcake recipe following the recipe card at the bottom of this post.

Fill the cupcake liners 3/4 full and bake them for 18-21 minutes, or until a toothpick comes out with a few moist crumbs. Remove the pan from the oven.

Let the cupcakes cool in the pan for 10 minutes, then remove them and place them on a wire rack to finish cooling.

If you’re in a rush, place the entire pan in the freezer for 30 minutes to accelerate the cooling process.

Step 3: Make the Lemon Cream Cheese Buttercream

While the cupcakes bake and cool, make the lemon cream cheese frosting.

If the frosting seems too thick, add an extra teaspoon of lemon juice. If it seems too thin, add in another 1/4 cup of powdered sugar.

Or if you’re unsure what consistency the frosting should be, check out my frosting consistency guide.

Once the frosting is made, stir it by hand with a rubber spatula to get it SUPER smooth.

Then place it in a piping bag fitted with a large round piping tip and seal the top with a rubber band.

Step 4: Cut out the Lemon Peel Heart Garnish

To make these cupcakes even cuter, I like to add a little lemon heart peel as a garnish.

This is optional, but who wouldn’t want these to be this cute?!?

Use a vegetable peeler to peel a few thin strips of skin from a lemon. Then use a small heart-shaped cutter to cut out 12 little hearts.

If you don’t have a heart-shaped cutter, you can also cut them out using a sharp, small knife.

Step 5: Fill and Frost the Lemon Cupcakes

If you choose to fill these cupcakes, remove the centers with a small sharp knife or a 3/4-inch circle cutter.

Fill each cupcake with 1 Tbsp of lemon curd. Filling the cupcakes is optional, but I think it really enhances their flavor.

You can use store-bought lemon curd, or you can make your own.

Then pipe a large dollop of lemon cream cheese buttercream on top of each cupcake.

Gently press a lemon peel heart onto each cupcake.

Use a microplane to top the cupcakes with lemon zest and add a sprinkle of poppy seeds, then enjoy!

Substitutions and Swaps – Lemon Poppy Seed Cupcakes

This cupcake recipe uses quite a few ingredients, and I know you might not have them all on hand. Or if you have food allergies or restrictions, I’ve got you covered.

Below are some swaps and substitutions that you can make.

• Granulated Sugar – I do not recommend reducing the amount of sugar or changing the type of sugar, as it will change the texture of these cupcakes.
• Fresh Lemon Zest – In a pinch, you could use lime zest. You can also increase the amount of lemon extract to 2 tsp in place of the lemon zest.
• Sour Cream – Full-fat yogurt, buttermilk, or an alternative yogurt or milk (almond, soy, oat) can also be used.
• 1 Large Egg – If you have an egg allergy, you can try using a flaxseed egg or a vegan egg replacer like this made by Bob’s Red Mill.
• Vegetable Oil – You can use any flavorless oil in this recipe, so canola or even sunflower oil would work great! I advise against olive oil because of its strong flavor.
• Cake Flour – This recipe turns out best with cake flour, but you can use a gluten-free flour blend or all-purpose flour if that’s all you have on hand.
• Lemon Curd – Filling these cupcakes is optional! You can also make your own or use jam. Blackberry or strawberry jam would be delicious.

Substitutions and Swaps – Lemon Buttercream Frosting

• Unsalted Butter – If you only have salted butter on hand, you can use it in place of the unsalted butter. Just be sure to omit the salt that this frosting recipe calls for. You can also use vegan butter in its place!
• Cream Cheese – The full fat cream cheese that comes in a block works best in this frosting.
• Fresh Lemon Juice and Zest – You can also use 2 tsp of lemon extract in place of the juice and zest in the frosting recipe. However, the flavor won’t be as bright.

How to Make Gluten-Free Lemon Poppy Seed Cupcakes

If you need to make gluten-free lemon poppy seed cupcakes, use gluten-free flour in place of the cake flour.

I prefer King Arthur’s gluten-free flour blend. In addition to swapping the flour, there are two additional steps you need to take when making gluten-free cupcakes.

Be sure to over-mix your batter and let it sit for at least 30 minutes before baking for best results.

Over-mixing gluten-free batter helps the cupcakes rise better as they bake and gives them a more tender crumb.

Letting the batter sit helps thicken the batter and prevents your cupcakes from having a gritty texture.

Lemon Poppy Seed Cupcake Troubleshooting & FAQs

While I’d love to think everyone’s cupcakes will turn out perfectly every time, I know that sometimes things don’t go to plan. Below are some tips and advice to help!

Why Didn’t My Cupcakes Rise? Why Are My Cupcakes Dense?

This can be caused by a few things. The most common is that either the ingredients weren’t all at room temperature, you over-mixed the batter after adding the flour, or your leavening agents are expired.

Using cold ingredients has a huge damper on how much baked goods rise. Make sure to set out cold ingredients ahead of time to let them come to room temperature.

Over-mixed batter can also create dense, chewy baked goods. Make sure that you mix the batter until it’s just combined once you’ve added the flour.

Expired baking powder is a sneaky one. Check the dates on your baking powder can. It can start to lose its leavening power after it’s been open for 6 months.

A quick and easy way to check your baking powder is to add a little bit to hot water. It should foam. If it doesn’t, it’s time to get some new baking powder.  

Why Did My Cupcakes Sink in the Middle? Why Did They Overflow on the Sides?

This can happen when the cupcakes are under-baked, overfilled, or if your oven runs cool.

One batch of batter should be the perfect amount to make 12 cupcakes, but it’s important that it’s evenly distributed between the liners. If they’re overfilled, they can overflow on the sides of the liners and/or sink in the middle.

Some cupcake pans and liners vary a bit in size, and this can also impact how the cupcakes bake up.

Another factor could be that your oven isn’t properly calibrated. I highly recommend getting an oven thermometer to make sure it’s baking at the right temperature.

Making These Lemon Cupcakes in Advance & How to Store Them

You can make these cupcakes in advance! Frosted and filled cupcakes can sit at room temperature for a few hours or be stored in the fridge for up to 5 days in an airtight container.

However, like all baked goods, these cupcakes taste best when they’re freshly baked!

They can also last up to a month in the freezer. If you plan to freeze them, I suggest waiting to fill and frost them until they’re thawed.

You can also make the buttercream ahead of time or save any leftovers. This buttercream frosting will last in the fridge for up to 2 weeks.

Be sure to give the frosting a good stir once it thaws to get the consistency nice and smooth again.

I like to store buttercream in a piping bag in the fridge. I find buttercream keeps its consistency well in piping bags and doesn’t require any mixing after it’s thawed.

Tips for Making the Best Lemon Poppy Seed Cupcakes

• Ingredients at room temperature mix together better. Set out any cold ingredients ahead of time.
• Properly measure the flour (spoon into the cup measure, then level) or use a kitchen scale to measure the dry ingredients.
• Mix the cupcake batter just until the ingredients are incorporated once you add in the flour. This will ensure the cupcakes are tender and fluffy.
• To make gluten-free lemon poppy seed cupcakes, swap in your favorite GF flour blend for the AP flour in this recipe. Be sure to over-mix your batter and let it sit for at least 30 minutes before baking for best results.
• Use a large cookie scoop to easily fill the cupcake liners. It also makes sure the cupcakes end up being the same height.
• Be careful not to overfill the cupcake liners! This can cause them to sink in the middle or explode over the sides of the liners.
• One batch of batter can also be used to make one 8×8-inch lemon poppy seed sheet cake. Bake it at 325°F/162°C for 33-38 minutes.

Let Me Know What You Think!

If you try this lemon poppy seed cupcake recipe, I’d love to hear what you think of it! Please leave a rating and comment below.

Don’t forget to tag me @chelsweets and use #chelsweets so that I can see your delicious creations on social media!

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