Gluten Free Pumpkin Whoopie Pies or Cupcakes (Paleo, AIP, Nut Free)

This Gluten Free Pumpkin Whoopie Pies recipe is a healthy gluten free fall dessert. It’s made of soft and chewy pumpkin sugar cookies which are filled with creamy and sweet pumpkin maple frosting. It’s delicious while also being dairy free and AIP/Paleo. And can easily be made into cupcakes.

gluten free whoopie pies on parchment paperDo pumpkin whoopie pies need to be refrigerated?

Yes, the whoopie pies need to stay refrigerated. You can store these on the counter for a few hours, but I find that the frosting tends to melt without refrigeration. Plus, the pumpkin makes this recipe very perishable. Keep in mind that this recipe tastes best when they are eaten the day they are made.

Can pumpkin whoopie pies be frozen?

I don’t think whoopie pies should be frozen. The frosting won’t freeze well. The texture would change and wouldn’t taste very well. 

close up of gluten free whoopie pie on parchment paper

What is the filling in whoopie pies made of?

The filling of our whoopie pies are made of AIP frosting, specifically pumpkin maple frosting.  

Is whoopie pie a cookie or a cake?

A whoopie pie is a cookie, in my opinion. Although the pumpkin cookies have the texture of a muffin top or cake.

dairy free whoopie pies on parchment paper

How to store pumpkin whoopee pies?

It’s best to store them in a airtight container and the bring them to room temperature before enjoying.


  • Beth Blends Nut/Cassava Free Grain Free Flour Blend
  • Gelatin: Make sure to use powdered gelatin.
  • Ground Cinnamon
  • Ground Ginger
  • Ground Cloves
  • Palm Shortening
  • Pumpkin Puree: Make sure to use pumpkin puree and not pumpkin pie filling.
  • Maple Syrup

Pumpkin Frosting Ingredients

  • Pumpkin Puree: Make sure to use pumpkin puree not pumpkin pie filling.
  • Vanilla Extract
  • Maple Sugar
  • Palm Shortening
  • Arrowroot Flour

How to make Gluten Free Pumpkin Whoopie Pies

1. Preheat oven to 350 degrees. Line baking sheet with parchment paper.

hand turning knob on oven range

2. Combine all the dry ingredients into a medium size mixing bowl.

woman with bag of flour putting flour into glass bowl

3. In a separate, small mixing bowl mix the palm shortening, pumpkin puree and maple syrup. 

woman pouring maple syrup into glass bowl

4. Add the shortening mixture to the dry ingredients then stir to combine.

woman pouring wet into dry ingredients with glass bowls

5. Using spoons or a cookie scoop, make 12 dough balls and place them at least 3 inches apart on the baking sheet. The dough will spread into round cookies and they need room to grow.

woman rolling dough in hands

6. Place the tray into the oven for about 10-12 minutes. Let cool completely before assembling the whoopie pies.

hand putting cookie sheet into oven

7. While the cookies are cooling, create the filling/frosting by combining all the ingredients in a small bowl. Then using a hand mixer, blend until smooth.

close up of hand stirring frosting with spoon

8. To assemble the whoopie pies, place a dollop of frosting on a cookie and then place another cookie on top of the frosting. Repeat until all the cookies are used. Then serve immediately.

woman assembling gluten free pumpkin whoopie pies

Tips for making the Best Gluten Free Pumpkin Whoopie Pies

  • The AIP/Paleo glaze won’t harden in warmer temperature or climates.
  • If you want to make muffins with this recipe, add to 6-8 muffin tins and bake for about 15 minutes.
  • You’ll welcome to skip the frosting and just enjoy the cookies. They taste like pumpkin spice sugar cookies but with the texture of a muffin top.
  • Store on the counter or in the refrigerator in an airtight container. Best if eaten the day of baking but must be eaten within 2-3 days.

If you like this recipe, then you’ll these pumpkin recipes.


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1 comment

  • RC

    After being on the AIP Protocol for 3 weeks I was hankering for a treat. After ordering Bethblends flour, I’ve made three batches of these whoopie pies. They are so filling and help me beat my cravings for hours. I absolutely love them!

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