Healthier Blueberry Whoopie Pies

These healthier blueberry whoopie pies are moist and fluffy with a creamy yogurt filling. They are made with less sugar, and the yogurt adds extra protein!

Half the Sugar Baker

As a New Englander, whoopie pies are a classic treat anytime of year. Instead of the traditional chocolate ones, I decided to make blueberry whoopie pies with a lemon filling to celebrate the flavors of summer! These whoopie pies are made from two super moist and fluffy cakes filled with a smooth and creamy yogurt filling. They are made with less sugar and processed ingredients, and the Greek yogurt filling adds extra protein!

healthier blueberry whoopie pie split in half

Why I love these healthier blueberry whoopie pies

Flavor: I love the combination of the sweet juicy blueberries with the fresh citrus flavor from the lemon zest. They’re an amazing match for summer! I also love how these whoopie pies aren’t too sweet and have the perfect tangy flavor from the yogurt filling.

Texture: These whoopie pies have such an amazing texture! They’re the perfect cross between a moist vanilla sheet cake and a fluffy blueberry pancake. I especially love the little bursts of juicy blueberries throughout the pies. The cakes are so good that sometimes I make them without the filling and eat them by themselves! The yogurt filling is thick and creamy, and definitely a little denser than the traditional marshmallow fluff filling.

Nutrition: Although I wouldn’t go as far as to call these whoopie pies a health food, they’re definitely healthier than traditional whoopie pies. They’re made with much less sugar and processed ingredients compared to most whoopie pies. The Greek yogurt filling also adds some extra protein! These whoopie pies are satisfying, and I love enjoying one for breakfast, snack, or dessert.

healthier blueberry whoopie pies on a plate with wire rack in background

What are whoopie pies?

As a New Englander, I thought whoopie pies were common knowledge! It wasn’t until later that I realized whoopie pies are a regional treat and many people have never had one. Whoopie pies are desserts made of two moist and fluffy cakes with a layer of cream filling in between. However, the cakes are baked on a baking sheet like cookies, not in a cake pan. Traditionally, whoopie pies are made with chocolate cakes and a marshmallow fluff filling, but so many different versions exist! I’ve seen pumpkin whoopie pies, red velvet whoopie pies, and apple cider whoopie pies. Fun fact: whoopie pies are the official state dessert of Maine!

Key ingredients in these healthier blueberry whoopie pies

  • All Purpose Flour
  • Baking Soda: Make sure it’s not expired!
  • Baking Powder: Make sure it’s not expired!
  • Unsalted Butter
  • Sugar
  • Eggs
  • Plain Greek Yogurt: Greek yogurt is used in both the cakes and the filling of these whoopie pies. I love how it adds some extra protein! You can use nonfat Greek yogurt or whole milk Greek yogurt. I don’t recommend substituting plain yogurt because it is thinner than Greek yogurt and might make the filling too runny.
  • Milk: You can use whatever milk you have on hand (nonfat, skim, whole milk, milk alternatives all work!) You could even use water in a pinch.
  • Lemon Juice or Vinegar: These acidic ingredients are extremely important, so don’t skip them! The acid reacts with the baking soda to create lots of bubbles and a super fluffy cake.
  • Blueberries: The key to this recipe is using good blueberries! You can use either fresh or frozen blueberries, just make sure that they’re sweet. If you are using frozen blueberries, do not let them thaw beforehand. Simply add them into the batter straight from the freezer.
  • Whipping Cream: Whipping cream helps give the filling a lighter texture and makes it slightly less tangy from the yogurt. I’ve also tried this recipe without the whipping cream, and it was also delicious! Feel free to skip the whipping cream but know that the filling will be slightly denser and have a stronger yogurt flavor.
  • Powdered Sugar: Powdered sugar dissolves much more easily than granulated sugar, which makes it perfect for a smooth filling. If you don’t wan’t to use powdered sugar, you could also try using other sweeteners like agave, honey, or maple syrup! I like to add the sweetener little by little and tasting until I reach my preferred level of sweetness.
  • Lemon Zest
two healthier blueberry whoopie pies on a plate

Tips and techniques for making these healthier blueberry whoopie pies

  • Make sure your baking soda and baking powder aren’t expired! These are common pantry staples, but they don’t last forever. If you have issues with flat or thin cakes, double check your leaveners.
  • Use room temperature ingredients (especially butter!) Using softened butter makes creaming so much easier. If your butter is cold, it might not cream completely and won’t emulsify. Room temperature ingredients also result in a better rise in the oven.
  • Creaming until light and fluffy: Make sure you cream the butter and sugar together until very light and fluffy. This incorporates air into the batter for fluffier whoopie pies!
  • Use Greek yogurt, not plain: Plain yogurt is thinner than Greek yogurt, which might make the filling too runny.
  • Strain the Greek yogurt: For a super thick and creamy filling, I recommend straining the Greek yogurt overnight to get rid of excess liquid. I like to line a sieve/colander with a cheese cloth or coffee filter and let the yogurt drip overnight.
  • Don’t skip the lemon juice! The acid reacts with the baking soda to make bubbles, which results in a super fluffy whoopie pie.
  • Don’t over mix: We want these whoopie pies to be super soft and tender, so make sure you don’t over work the batter which can develop too much gluten. Gently fold the wet and dry ingredients together until everything is just combined. It’s ok if there are some small lumps!
  • Don’t over bake: These whoopie pies won’t get very brown on top. Instead, to tell if they’re ready, lightly poke one. Once fully baked, the indent should bounce right back!
  • Wait to fill until ready to serve: To prevent soggy whoopie pies, I recommend waiting to fill these whoopie pies until right before serving.
healthier blueberry whoopie pie on a wire rack

Variations and ingredient substitutions

  • Milk: Feel free to use whatever milk you have on hand. Nonfat, skim, whole milk, and milk alternatives all work in this recipe. You could even use water in a pinch!
  • Buttermilk: Instead of the Greek yogurt, milk, and lemon juice, you could substitute 1 cup + 2 tablespoons buttermilk.
  • Other fruits: Instead of blueberries, you could try other chopped fruits like strawberries or peaches. Just make sure you slice them into small pieces so they don’t sink to the bottom of the cakes.
  • No whipping cream: Whipping cream helps give the filling a lighter texture and makes it slightly less tangy from the yogurt. I’ve also tried this recipe without the whipping cream, and it was also delicious! Feel free to skip the whipping cream but know that the filling will be slightly denser and have a stronger yogurt flavor.
  • Ricotta filling: Instead of Greek yogurt, you could also try making a ricotta filling (like a cannoli!) Instead of Greek yogurt, substitute whole milk ricotta that has been strained overnight.
  • Powdered sugar alternatives: Instead of powdered sugar, feel free to use other sweeteners like agave, honey, or maple syrup.
healthier blueberry whoopie pie on a plate

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Healthier Blueberry Whoopie Pies

These healthier blueberry whoopie pies use less sugar and butter than traditional whoopie pies, but they're still super fluffy and moist. The delicious lemon cream filling is made from Greek yogurt, not marshmallow fluff for a healthier twist! These whoopie pies are the perfect way to celebrate the flavors of summer.
Prep Time20 minutes
Cook Time10 minutes
Total Time30 minutes
Course: Breakfast, Dessert, Snack
Keyword: blueberry, healthy, pie, summer, whoopie pie
Servings: 12 whoopie pies (24 halves)
Author: Half the Sugar Baker

Ingredients

For the whoopie pies:

  • 2 cups all purpose flour
  • 1 ¼ teaspoons baking soda
  • 1 teaspoon baking powder
  • ¼ teaspoon salt
  • 6 tablespoons unsalted butter room temperature
  • 1/2 cup granulated sugar
  • 2 eggs room temperature
  • 3/4 cup plain Greek yogurt
  • 1/3 cup milk
  • 1 tablespoon lemon juice or vinegar
  • 1 1/2 teaspoons vanilla extract
  • 1 1/4 cups blueberries fresh or frozen

For the Greek yogurt filling:

  • 1/2 cup whipping cream optional
  • 3 1/2 cups Greek yogurt preferably strained overnight
  • 1 cup powdered sugar add more to taste
  • 1 tablespoon vanilla extract
  • 2 tablespoons lemon zest

Instructions

  • Preheat oven to 375ºF. Line two baking sheets with parchment paper.
  • In a medium bowl, whisk together the flour, baking soda, baking powder, and salt.
  • In a large bowl, beat together the butter and sugar until light and fluffy. Beat in the eggs one at a time until well combined. Add the yogurt, milk, lemon juice, and vanilla extract and beat until smooth. Pour the dry ingredients into the wet ingredients and fold gently until just combined. Gently stir in the blueberries, being careful not to over mix.
  • Spoon the batter onto baking sheet, about 2 tablespoons of batter per cake. Leave room for spreading. Bake for 11 minutes, or until the cakes bounce back when lightly poked. Let cakes cool on pan for 5 minutes before transferring to a wire rack to cool completely.

To make the filling:

  • In a large bowl, beat the whipping cream until it reaches medium peaks. Add the yogurt, powdered sugar, vanilla extract, and lemon zest and beat until light and fluffy.
  • Once the cakes have cooled completely, top half of them with 3-4 tablespoons of the filling and cover with the remaining cakes. Enjoy!
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