finished product of lemon poppy seed whoopie pies with lemon slices as garnish

Lemon Poppy Seed Whoopie Pies

Lemon Poppyseed anything is always such a favorite of mine. Cupcakes, muffins, a loaf, whatever it is I’m in. The idea for this recipe came from wanting to bake something with lemons and poppy seeds but didn’t want to bake it in the traditional sense that we’re all familiar with. That’s when it hit me…why have I never seen a Lemon Poppyseed Whoopie Pie?! So that’s what we’re here to make together today. I hope you enjoy this recipe as much as I do!

close up of finished lemon poppy seed whoopie pies with hand holding one up to the camera

How To Make Lemon Poppy Seed Whoopie Pies

This recipe comes together super easy and the batter for the pies is all brought together in one bowl. Easy peasy. It’s important to use fresh ingredients as much as you can in recipes. That’s why I recommend using fresh lemon juice and zest in this delicious treat.

Lemon Poppy Seed Whoopie Pie Filling

I wanted to try to keep the filling somewhat traditional to the typical chocolate whoopie pie filling. That’s why I used a combination of butter, fluff, confectioner’s sugar, and vanilla. Of course, to keep it on par with our lemon them going on, I added lemon juice and zest as well. The filling is super easy to make and can be made with an electric mixer, stand mixer, or by hand.

lemon poppy seed whoopie pie batter mixed together

More Recipes Like Lemon Poppy Seed Whoopie Pies

How To Store Lemon Poppy Seed Whoopie Pies

These Whoopie Pies should be kept and stored in the fridge sealed in a ziplock bag or air-tight container. These will stay fresh for up to one week in the fridge or up to 3 months in the freezer. If these whoopie pies are kept out too long or become too warm the filling will become a bit messy.

lemon poppy seed whoopie pie filling with lemon zest on top

Tips & Tricks For Making Lemon Poppy Seed Whoopie Pies

  • Consistency – One of the most important parts of making whoopie pies of any flavor is to try your best to keep the size of the whoopie pies as consistent as possible so that they sandwich together nicely and the sides match up. Using a cookie scoop to accurately measure the size of each whoopie pie will help immensely.
  • Filling – Filling the whoopie pies is one of the last steps to assembling your delicious treats. Using a cookie scoop for this step as well will help keep the filling amount consistent for each whoopie pie. It’s best to fill one whoopie pie, place the top on it, and then check how that specific amount of filling turned out. From there you can add more or less to the rest of the whoopie pies after experimenting with the first one.
  • Even Spacing – Since whoopie pies spread and rise in the oven, it’s important to leave enough space between each one to prevent them from touching or forming together in the oven. You should leave about 2 inches of space between each whoopie pie dollop before baking.
  • Cooling Time – Another important detail in this recipe is to be sure that the whoopie pies are completely cooled before filling them. If the whoopie pies are still warm while being filled, the filling will melt into the shells and become a sticky mess. Use a wire rack to ensure a proper cool for all of your whoopie pie shells.

Lemon Poppy Seed Whoopie Pies

Recipe by Maddison Koutrouba –
5.0 from 3 votes


Cooking time


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  • 2 cups all-purpose flour

  • 1/2 tsp. baking soda

  • 1/4 tsp. salt

  • 3/4 cups sugar (plus extra for sprinkling on top)

  • 1/4 cup vegetable oil

  • 1 egg, room temperature

  • 1/2 cup buttermilk

  • zest of two lemons

  • 1 1/2 Tbsp. poppy seeds

  • Lemon Whoopie Pie Filling
  • 1/4 cup unsalted butter, room temperature

  • 1 cup marshmallow fluff

  • 2 1/2 cups powdered sugar

  • 1 Tbsp. heavy cream

  • juice of half a lemon

  • zest of half a lemon

  • 2 Tbsp. butter (for brushing on top)


  • Preheat the oven to 350 degrees and line a cookie sheet with parchment paper. Set aside.
  • In a medium-sized bowl, whisk together the flour, baking soda, and salt. Set aside.
  • In a separate, large bowl, whisk together the sugar, oil, and egg. Whisk until smooth.
  • Add the dry ingredients and buttermilk to the bowl of wet ingredients. Alternate adding the dry ingredients and buttermilk starting and ending with the dry ingredients. Mix between each addition until the mixture is just combined. Stop mixing when the batter is almost together. Add in the zest of two lemons and poppy seeds. Use a silicone spatula to combine everything together nicely.
  • Use a cookie scoop to scoop about 3-4 Tbsp. of batter per whoopie pie dollop. These should be 2″ apart on the prepared cookie sheet.
  • Bake for 10-12 minutes or until barely golden brown on the bottom and edges. Tap the top of the whoopie pie to test if it’s finished baking. It shouldn’t sink in and instead have a slight spring back.
  • Allow the whoopie pie shells to cool completely on a wire rack before filling.
  • Lemon Whoopie Pie Filling
  • To make the filling, use a stand mixer fit with the whisk attachment or an electric mixer to combine the butter, and fluff together until smooth.
  • Add the powdered sugar, heavy cream, lemon juice, and zest. Mix until fully combined and smooth.
  • Assembling Lemon Poppy Seed Whoopie Pies
  • Brush melted butter on top of each whoopie pie shell then sprinkle granulated sugar on top of each one. Repeat this step until all of the whoopie pies are perfectly coated.
  • Scoop a generous amount of filling on the bottom side of half the whoopie pies then top with another shell.
  • Enjoy!

Did you make this recipe?

Tag @thesqueakymixer on Instagram! I love to see what you all create.

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