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close up of 2 gluten free whoopie pies on wire rack. Piping bag with frosting in front and 1 whoopie pie in far back. White marble background.

Gluten-Free Whoopie Pies

Author: Janet Harlow
Course: Baked Goods
Cuisine: American
Servings: 12
These gluten-free whoopie pies have a dark, moist chocolate cake and creamy buttercream filling. If you prefer the traditional marshmallow filling, the recipe is included too
5 from 2 votes
Prep Time 30 mins
Cook Time 10 mins
Total Time 40 mins


Gluten-Free Chocolate Cake

  • 3/4 c gluten-free flour blend*
  • 3/4 unsweetened cocoa powder
  • 1/2 tsp baking powder
  • 1/4 tsp baking soda
  • 1/8 tsp salt
  • 3 large eggs room temperature
  • 2/3 c unsweetened dairy-free milk room temperature
  • 2/3 c oil light olive, sunflower, avocado, canola
  • 1 tsp vanilla extract or powder
  • 1 c sugar

Vanilla Buttercream Filling

  • 1 stick 4oz unsalted butter, room temperature
  • 1 1/2 c powdered sugar
  • 1 tsp vanilla extract or bean paste
  • 2 tps milk or milk substitute

Marshmallow Filling

  • 2 large egg whites room temperature
  • 1/4 c + 2 Tbsps sugar NOT powdered
  • 3 Tbsps light corn syrup
  • 1/2 tsp vanilla extract


  • You will need a muffin top pan/whoopie pie pan (same thing).
  • Pre-heat the oven to 325°F.
  • If the eggs are cold, place in a bowl of warm water while preparing the other ingredients.
  • Sift the flour, cocoa powder, baking powder, baking soda, salt and espresso powder (If using) into a mixing bowl. Stir with a whisk to combine well.
  • If the milk is cold, heat in the microwave for 10 seconds to take the chill off. In a small bowl, very lightly beat the the eggs, milk, oil, vanilla and sugar.
  • Add the liquid ingredients to the dry and stir until mostly smooth. Over-mixing will create too many air bubbles which will cause uneven rising and dry cake.
  • Fill each well with about 3 Tbsps batter. Smooth the top and spread it evenly to the edges. Gently, shake the pan side to side and forward and back to help spread it evenly,
  • Bake 10 minutes or until the top is set and bounces back from a gentle tap.
  • Cool in the pan for 5 minutes, then transfer to a wire rack to cool completely. These do need to cool for an hour before handling or the top is too sticky,
  • Make the FillingChoose either the Buttercream Filling OR Marshmallow Filling

Buttercream Filling

  • This buttercream filling can be made ahead of time. If using within 24 hours, leave at room temp, otherwise, refrigerate and pull it out about 2 hours before using.
  • If your powdered sugar is very lumpy, I suggest sifting it. I use C&H and rarely sift, and get smooth creamy results.
  • Using an electric mixer, beat the butter for 30 seconds until creamy.
  • Add half of the powdered sugar and beat on low until incorporated. Add the remaining powdered sugar and beat on low until incorporated.
  • Scrape down the sides and bottom of the bowl. Add the milk and vanilla and beat on high for 15- 20 seconds.
  • See above for flavor options or more frosting recipes.
  • For easiest assembly, place the buttercream in a pastry piping bag fitted with a tip.

Marshmallow Filling

  • This marshmallow filling should be used immediately, so it its best to wait to make it until the cakes are almost cooled.
  • Place the egg whites, sugar and corn syrup in the top of a double boiler over rapidly boiling water. Beat constantly with an electric mixer until soft peaks form. It should take 3-4 minutes.
  • Transfer the mixture to a large mixing bowl or the bowl of a stand mixer.
  • Beat on medium high speed, with a whisk attachment if you have it, until soft peaks form. It should take less than a minute.
  • Transfer to a pastry piping bag fitted with a tip for easiest assembly.

Assemble the Whoopie Pies

  • Take one of the little cakes and add frosting to the flat bottom. Gently press another little cake on top. ENJOY!


*I tested this recipe with King Arthur Measure for Measure Flour which contains xanthan gum. If you use a gluten-free flour blend without binders like xanthan gum, guar gum or inulin, add 1/2 tsp xanthan gum.
Did you make this recipe?Let me know how it was! Tag @chefjanetk on Instagram.