This Lemon Poppy Seed Cupcakes with Poppy Seed Pudding recipe yields moist lemon cupcakes dotted with poppy seeds, topped with lemon cream cheese buttercream and filled with poppy seed pudding. These are really lemon AND poppyseed cupcakes because you get an equal amount of each flavor! I use plenty of lemon juice, lemon zest and poppy seeds to flavor this lemon poppy seed cupcake recipe.
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I've always loved lemon poppy seed, but I feel like most recipes yield a lemon dessert that has just a whisper of poppy seed. Poppy seeds DO have a flavor of their own! You just have to use quite a bit of them to taste it. So, I took the poppy seed filling recipe from my homemade poppy seed kolaches to fill these cupcakes for a more potent poppy seed flavor. The lemon cream cheese frosting is adapted from Two Sisters Crafting, and brings just the right amount of zippy lemon flavor to balance out the sweetness.
Lemon pairs so well with earthy flavors like poppy seed. I also really loved it in my lemon pepper sugar cookies, which sounds wild, but just trust me. If you like lemon-only desserts I also have a bunch of those around here, from tarts to macarons.
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Why you'll love this recipe
- You can actually taste the poppy seed in these! They're earthy and pair so well with the tart lemon.
- You don't need a stand mixer! The cupcake batter can be made with a whisk and the buttercream can be made with hand beaters.
- The lemon buttercream has a great tart natural lemon flavor and pairs beautifully with tangy cream cheese.
Ingredients
- Poppy seeds flavor the pudding and cupcakes.
- Whole milk adds moisture to the pudding.
- Granulated sugar sweetens the pudding and cupcakes.
- Cornstarch helps thicken the poppy seed pudding.
- Vanilla extract and kosher salt round out the flavor profile.
- Egg helps thicken and add structure to the pudding and cupcakes. Use room temperature eggs so they incorporate better.
- Lemon zest, lemon juice and lemon extract bring lots of lemon flavor.
- All-purpose flour provides a tender crumb for the cake.
- Baking powder and baking soda give the cakes lift.
- Oil brings richness to the cake and helps it stay moist for longer. I use avocado oil, but any neutral-flavored oil like canola oil, vegetable oil or grapeseed oil will work here.
- Sour cream adds richness and tang to the cake.
- Unsalted butter is the base of the buttercream.
- Powdered sugar sweetens the buttercream.
- Cream cheese flavors the buttercream.
See recipe card below for a full list of ingredients and measurements.
Substitutions and variations
Here's how to customize this easy lemon poppy seed cupcakes recipe to your liking:
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- Muffins — skip the pudding and frosting to make lemon poppy seed muffins.
- Cupcake liners — you can make these without cupcake liners, but be sure to generously grease the pan cavities.
- Butter — swap half or all of the oil in the cake for unsalted butter, if desired.
- Greek yogurt — if you don't have sour cream you can swap for greek yogurt. Add 1 tablespoon more oil to make up for the loss of fat.
- Cake — instead of baking in cupcake pans, you can bake the batter in a 9x13 pan.
- No lemon extract — if you don't have lemon extract, be sure to add 1 extra tablespoon of lemon zest to the batter.
- Cake flour — if using cake flour, use 2 tablespoon more cake flour than what is called for in all-purpose flour.
This recipe has not been tested with any substitutions or variations. If you try any, please let me know how it turned out by commenting below!
How to make Lemon Poppy Seed Cupcakes Step-By-Step
Step 1: Warm the milk on the stove or in the microwave just until warm. Do not let it boil. Add the poppy seeds, cover and let sit for at least 2 hours or overnight in the refrigerator. In a heavy-bottomed pot, whisk together the sugar and cornstarch to remove any lumps. Then add the poppy seeds and the milk they were soaked in, as well as the beaten egg.
Step 2: Cook over low heat, stirring constantly, until thickened, about 10-15 minutes. Remove from the heat and add the butter, vanilla and salt and stir until combined and the butter melts in. Transfer to a bowl or a sheet pan, and cover with plastic wrap to prevent a skin from forming. Chill in the refrigerator until completely cool. This could take up to 2 hours, or less if you spread it thin on a sheet pan. When the pudding is completely chilled, stir in the lemon juice.
Step 3: Preheat the oven to 350°F. Fill a 12-cavity muffin tin with cupcake liners. Spray the cupcake liners with oil. In a medium bowl, rub together the sugar and lemon zest with your fingers to express the oils for more flavor. Whisk in the flour, salt, baking powder, baking soda and poppy seeds. Set aside.
Step 4: In a large bowl, whisk together the eggs, sour cream, oil, lemon juice, vanilla and lemon extract. Add the dry ingredients to the wet ingredients and fold with a rubber spatula just until there are no longer any streaks of flour. Using a large cookie scoop or a ¼-cup measuring cup, scoop batter into each cavity of the prepared pan just ¾ of the way up the sides. Bake for 15-19 minutes or until a toothpick inserted in the center comes out clean. Remove to a wire rack to cool completely before frosting.
Step 5: In the bowl of a stand mixer fitted with the paddle attachment, or in a large bowl with beaters, add the cream cheese and beat on medium speed until smooth. Make sure there are no more lumps. Scrape down the bowl a few times to be sure before removing the beaten cream cheese to a separate bowl. In the bowl you just used, add the butter and beat for 3 minutes or until lightened in color and fluffy. Add the cream cheese back to the bowl with the butter and beat to combine. Add half of the powdered sugar and beat on low speed until combined. Mix in the fresh lemon juice, lemon zest, salt and optional citric acid. Mix in the remaining powdered sugar until incorporated.
Step 6: Core out the centers of the cooled cupcakes with an apple or cupcake corer or small paring knife. Spoon or pipe some of the poppy seed pudding into the center of the cupcake. Spoon or pipe on a dollop of the frosting. Use the back of a spoon to make a divot in the middle. Spoon or pipe more of the poppy seed pudding into the divot. Garnish with more poppy seeds, if desired.
Top tips
- For best results, don't skip spraying your cupcake liners! It makes for a much easier release.
- Use an oven thermometer to double check your oven temperature. Mine varies by 50 degrees sometimes!
- A piping bag and a plain large round piping tip make for easier and cleaner frosting.
More recipes you'll love
Lastly, if you make this Lemon Poppy Seed Cupcakes with Poppy Seed Pudding recipe be sure to leave a comment or give it a rating. I love to see when people make my recipes, so please tag me @youthsweets on Instagram if you post!
📖 Recipe
Lemon Poppy Seed Cupcakes with Poppy Seed Pudding
Equipment
- Hand beaters
Ingredients
Poppy seed pudding
- ½ cup poppy seeds whole, not ground (72g)
- ½ cup + 2 tablespoon whole milk (147g)
- ½ cup + 2 tablespoon granulated sugar 125g
- 2 tablespoon cornstarch 17g
- 1 egg beaten
- 1 tablespoon unsalted butter (14g)
- 1 teaspoon vanilla extract
- ¼ teaspoon kosher salt half if using table salt
- 2 tablespoon lemon juice
Lemon poppy seed cupcakes
- 2 tablespoon lemon zest grated, then measured, then very finely chopped (6g)
- 1 cup granulated sugar (200g)
- 1¾ cups all-purpose flour (220g)
- 1 ½ teaspoon kosher salt half if using table salt
- 1½ teaspoon baking powder
- ½ teaspoon baking soda
- 2 tablespoon poppy seeds (19g)
- ⅔ cup oil (140g)
- 2 large eggs
- ¾ cup sour cream (173g)
- 2 tablespoon lemon juice freshly-squeezed
- 1 tablespoon vanilla extract
- 1 ½ teaspoon lemon extract
Lemon cream cheese buttercream
- 8 oz cream cheese softened (224g)
- ½ cup unsalted butter room temperature (1 stick, 113g)
- 5 cups powdered sugar (625g)
- ¼ cup lemon juice freshly-squeezed (57g)
- 1 tablespoon lemon zest grated, then measured, then very finely chopped (3g)
- ¼ teaspoon kosher salt half if using table salt
- ¼ teaspoon citric acid optional
Instructions
Do ahead
- Warm the milk on the stove or in the microwave just until warm. Do not let it boil. Add the poppy seeds, cover and let sit for at least 2 hours or overnight in the refrigerator.
Make the poppy seed filling
- In a heavy-bottomed pot, whisk together the sugar and cornstarch to remove any lumps. Then add the poppy seeds and the milk they were soaked in, as well as the beaten egg.
- Cook over low heat, stirring constantly, until thickened, about 10-15 minutes. Remove from the heat and add the butter, vanilla and salt and stir until combined and the butter melts in.
- Transfer to a bowl or a sheet pan, and cover with plastic wrap to prevent a skin from forming. Chill in the refrigerator until completely cool. This could take up to 2 hours, or less if you spread it thin on a sheet pan. When the pudding is completely chilled, stir in the lemon juice.
Make the cupcakes
- Preheat the oven to 350°F. Fill a 12-cavity muffin tin with cupcake liners. Spray the cupcake liners with oil.
- In a medium bowl, rub together the sugar and lemon zest with your fingers to express the oils for more flavor. Whisk in the flour, salt, baking powder, baking soda and poppy seeds. Set aside.
- In a large bowl, whisk together the eggs, sour cream, oil, lemon juice, vanilla and lemon extract. Add the dry ingredients to the wet ingredients and fold with a rubber spatula just until there are no longer any streaks of flour.
- Using a large cookie scoop or a ¼-cup measuring cup, scoop batter into each cavity of the prepared pan just ¾ of the way up the sides.
- Bake for 15-19 minutes or until a toothpick inserted in the center comes out clean. Remove to a cooling rack to cool completely before frosting.
Make the frosting
- In the bowl of a stand mixer fitted with the paddle attachment, or in a large bowl with beaters, add the cream cheese and beat on medium low until smooth. Make sure there are no more lumps. Scrape down the bowl a few times to be sure before removing the beaten cream cheese to a separate bowl.
- In the bowl you just used, add the butter and beat for 3 minutes or until lightened in color and fluffy. Add the cream cheese back to the bowl with the butter and beat to combine.
- Add half of the powdered sugar and beat until combined. Mix in the lemon juice, lemon zest, salt and optional citric acid. Mix in the remaining powdered sugar until incorporated.
Assemble
- Core out the centers of the cooled cupcakes with an apple corer or small paring knife. Spoon or pipe in some of the poppy seed pudding.
- Spoon or pipe on a dollop of the frosting. Use the back of a spoon to make a divot in the middle. Spoon or pipe more of the poppy seed pudding into the divot. Garnish with more poppy seeds, if desired.
Video
Notes
Nutrition
Originally published 3/19/2026.
