These gluten-free pumpkin whoopie pies are made with a thick cream cheese frosting sandwiched between two moist, spiced pumpkin cookies. It’s a fall dessert dream! (Dairy-free option!)

If you’re searching for a gluten-free pumpkin whoopie pie recipe to make this season, you’ve found it! Check out this post to get my expert tips on creating fluffy whoopie pies with the perfect texture.

An overhead view of gluten-free pumpkin whoopie pies in a baking dish
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The first time I had a pumpkin whoopie pie I remember thinking it was the best thing I had ever eaten! Not just one of the best pumpkin baked goods or best gluten free desserts, but the most delicious creation possible!

Obviously, cream cheese frosting and pumpkin were simply made for each other. I often use dairy-free cream cheese and vegan butter in the filling to keep these dairy-free. (PS if you love pumpkin and cream cheese frosting try these gluten-free pumpkin bars or this gluten-free pumpkin roll!)

I’ll be honest, it was a little tricky to make gluten-free pumpkin spice whoopie pies that are as delicious as traditional whoopie pies. But after many attempts, I finally got the cake-y structure I was looking for!

PS – you also might like these gluten-free oatmeal cream pies!

The resulting cookie is lightly spiced and holds up beautifully with the lucious cream cheese filling. (You might also like these gluten-free pumpkin muffins.)

Making pumpkin whoopie pies is definitely on my fall traditions list, along with caramel corn, cornbread & chili, and spiced apple cider. They need to be made at least once each year, if not more!

If you have never had a whoopie pie, they’re sure to become one of your favorite fall treats as well!

Why You’ll Love this Recipe

  • Moist and fluffy
  • Rich cream cheese frosting
  • Great for fall parties
  • Portable, handheld treat
  • Classic fall flavors

Looking for more pumpkin baked goods? Try these recipes for gluten-free pumpkin cookies, gluten-free pumpkin donuts, pumpkin creme brulee and gluten-free pumpkin pie. You also might like this full collection of gluten-free pumpkin recipes.

For breakfast/quick bread recipes try these gluten-free pumpkin pancakes, gluten-free pumpkin muffins and gluten-free pumpkin chocolate chip bread.

Ingredients You’ll Need

For the Whoopie Pies

Here’s what you’ll need to make these whoopie pies:

Gluten-free pumpkin whoopie pie ingredients on a counter top
  • Oil: I like to use a neutral oil like vegetable oil for the best consistency and flavor in these gluten-free pumpkin whoopie pies.
  • Spices: Pumpkin pie spice is a key ingredient that makes these whoopie pies the delicious fall treat we all know and love!
  • Pumpkin: Use real canned pumpkin for this recipe (pumpkin puree), not pumpkin pie filling!
  • Brown sugar: Brown sugar adds sweetness and a touch of molasses flavor.
  • Vanilla: I always prefer real vanilla extract, but you can use imitation vanilla, too.
  • Gluten-free flour: Make sure you use a high-quality 1:1 gluten-free baking flour that includes xanthan gum for the best results.
  • Sugar: White sugar adds more sweetness to these delicious gluten-free pumpkin whoopie pies.
  • Eggs: Eggs are essential for binding the batter and adding richness and flavor.
  • Baking powder/baking soda: Baking soda and baking powder are both important for creating light, fluffy gluten-free whoopie pies with the perfect rise.
  • Salt: Salt balances the sweetness and enhances the flavor of the whoopie pies.

You also might like these soft pumpkin chocolate chip cookies!

For the Cream Cheese Frosting

Here’s what you’ll need to make this delicious and rich cream cheese frosting!

Frosting ingredients on a counter top
  • Powdered sugar: Powdered sugar is the essential base to this frosting recipe.
  • Butter: Use real unsalted butter for the most delicious cream cheese frosting. Set your stick of butter out in advance so it’s at room temperature when you make the frosting.
  • Cream cheese: Room temperature cream cheese will result in a more creamy, smooth frosting.
  • Vanilla: Use real vanilla extract for the best cream cheese frosting!

Dairy-Free Option

MAKE IT DAIRY-FREE: You can use dairy-free cream cheese and vegan butter in the filling to make these dairy-free. I prefer using Kite Hill cream cheese and Earth Balance buttery sticks. 

How to Make Gluten-Free Pumpkin Whoopie Pies

Oil and sugar in a mixing bowl, and pumpkin and eggs added into the bowl
  • In a large bowl, whisk together the oil, brown sugar and granulated sugar.
  • Add the pumpkin, eggs, and vanilla and mix very well to combine.
Whoppie pie ingredients mixed in a bowl and whoopie pie batter scooped onto a baking sheet
  • Add the dry ingredients to the wet ingredients and stir until the dough is thoroughly combined and smooth.
  • Drop the cookie batter by rounded tablespoon-sized scoops onto a parchment paper lined baking sheet, spacing scoops at least 2″ apart.
Baked whoopie pies on a baking sheet, and whoopie pies cooling on a wire rack
  • Bake for 10-12 minutes.
  • Let the cookies cool on the baking sheet completely before filling.
Frosting in the bowl of a stand mixer, and whoppie pies on a wire cooling rack with frosting on one half
  • Using a hand or stand mixer, beat together the butter and cream cheese until combined. Add the powdered sugar and vanilla.
  • Beat on low then switch to high for about three minutes or until light and creamy. Scrape down the sides and bottom of the bowl then mix for another 30 seconds or so.
  • Pipe or spread the filling onto the bottom of one cooled pumpkin cookie, then top with another cookie. Enjoy these delicious whoopie pies!
Pumpkin whoopie pies arranged in a baking dish

Storage Instructions

Store leftovers in the refrigerator in an airtight container for up to 5 days. You also might like these pumpkin spice macarons!

FAQs

What is the filling in whoopie pies made of?

Whoopie pie filling varies depending on the recipe and flavor of the whoopie pie. For this recipe, I used a rich, thick, cream cheese frosting. Other recipes might call for marshmallow cream, marshmallow fluff, chocolate frosting, or vanilla frosting.

What is the difference between a whoopie pie and cake?

A whoopie pie is similar in texture and flavor to a slice of cake or a cupcake, but the frosting is sandwiched in the middle of two cake-like cookies, rather than being piled on top. You can consider them a more portable version of sliced cake!

What is whoopie in whoopie pie?

According to the rumors, whoopie pies were named after some Amish men who would yell out, “Whoopie!” when they’d see this treat in their lunch.

A closeup shot of pumpkin whoopie pies with a bite taken out of one

More Gluten-Free Pumpkin Desserts

I hope you love this pumpkin whoopie pie recipe as much as we do! If you try these gluten-free pumpkin whoopie pies, be sure to leave me a comment/rating below. I’d love to hear from you!

A close up of whoopie pies in a baking dish
5 from 20 votes

Gluten-Free Pumpkin Whoopie Pies

Prep Time 20 minutes
Cook Time 20 minutes
Cooling Time 20 minutes
Total Time 1 hour
Servings 16 whoopie pies
These gluten-free pumpkin whoopie pies are made with a thick cream cheese frosting sandwiched between two moist, spiced pumpkin cookies. It's a fall dessert dream!

Ingredients

Dry Ingredients:

  • 1 1/2 cup gluten-free 1:1 baking flour 225 grams
  • 1 teaspoons baking powder
  • ¾ teaspoons baking soda
  • ¾ teaspoon salt
  • 2 teaspoons pumpkin pie spice
  • ½ teaspoon ground cinnamon

Other:

  • cup vegetable oil 150 grams
  • ¾ cup light brown sugar 150 grams, firmly packed
  • ¼ cup granulated sugar 50 grams
  • 1 cup pumpkin puree 225 grams (100% pumpkin)
  • 2 eggs
  • 1 ½ teaspoon vanilla extract

For the Filling:

  • ½ cup butter room temperature
  • 8 oz cream cheese room temperature
  • 3 cups powdered sugar 340 grams
  • 1 teaspoon vanilla
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Instructions 

  • Preheat the oven to 375F and line a baking sheet with parchment paper. Set aside.
  • In a medium bowl, whisk together the dry ingredients. Set aside.
  • In a large bowl, whisk together the oil, brown sugar and granulated sugar. Add the pumpkin, eggs, and vanilla and mix very well to combine.
  • Add the dry ingredients to the wet ingredients and stir until the dough is thoroughly combined and smooth.
  • Drop batter by rounded tablespoon-sized scoops onto a parchment paper lined baking sheet, spacing scoops at least 2″ apart. Bake for 10-12 minutes.
  • Let the cookies cool on the baking sheet completely before filling.

Make the Frosting:

  • Using a hand or stand mixer, beat together the butter and cream cheese until combined. Add the powdered sugar and vanilla.
  • Beat on low then switch to high for about three minutes or until light and creamy. Scrape down the sides and bottom of the bowl then mix for another 30 seconds or so.
  • Pipe or spread the filling onto the bottom of one cooled pumpkin cookie, then top with another cookie. Enjoy!
  • Store leftovers in the refrigerator in an airtight container for up to 5 days.

Notes

MAKE IT DAIRY-FREE: You can use dairy-free cream cheese and vegan butter in the filling to make these dairy-free. I prefer using Kite Hill cream cheese and Earth Balance buttery sticks. 

Nutrition

Calories: 301kcal | Carbohydrates: 46g | Protein: 3g | Fat: 12g | Saturated Fat: 7g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 3g | Trans Fat: 0.2g | Cholesterol: 50mg | Sodium: 265mg | Potassium: 144mg | Fiber: 1g | Sugar: 36g | Vitamin A: 2781IU | Vitamin C: 1mg | Calcium: 51mg | Iron: 1mg

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Hi, I'm Erin!

BS Food Science,

MS Nutrition

I believe you can make amazing, gluten-free food with everyday ingredients that everyone will enjoy. I'm here to share my tried-and-true recipes with you!

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Comments

  1. Do you have a chocolate version? I would be interested in trying to make a chocolate version for Monday’s eclipse!

    1. Hi Stacey, we’re sorry we didn’t respond in time for the eclipse. We hope you had a fun viewing! We don’t currently have a chocolate whoopie pie recipe on the website, but we love the idea!

  2. 5 stars
    I have made these 3 times in the past 2 months and still get requests to make them from family and friends. They are the perfect little holiday treat so moist and full of flavor! I add almost 2 tsp of cinnamon to the cream cheese frosting and highly recommend 🙂 thank you for a great recipe! No one would know they are gluten free

  3. 5 stars
    Everyone loved these. I made a double recipe, and I don’t think a single recipe would have been enough. I used Red Mill Gluten Free flour, and for the filling I used Miyoko’s Dairy Free Cream Cheese. I ended up using just regular butter. The filling tasted too lemony with the dairy free cream cheese on day 1, but by day 2 the flavors blended nicely and tasted every bit as good as the full gluten and full dairy counterpart.

  4. 5 stars
    I used Bob’s Red Mill 1 to 1 g/f flour, and even though the batter was a little looser than I expected they did bake up nicely and are very tasty. I may add a bit more flour next time to see if I will get a thicker cookie. I’m new at this g/f baking thing, so I expect there will be some trial and error, but I am quite happy with this first attempt at whoopie pies! And the filling is scrumptious!

  5. 5 stars
    Super yummy! I used KA measure for measure. I attempted to eat one sandwich style and all the yummy filling squished out, so we are just going to eat them open faced. Not sure if I made them too big, I ended up with 14 pairs of cookies and WAY more filling than would fill 14 pies. So it worked out well open faced – gotta use up all that delicious filling!

  6. 5 stars
    I made these for a gluten-intolerant co-worker, and based on past experience with baking gluten-free, didn’t have high expectations. To say these pumpkin whoopie pies exceeded my- expectations is an understatement – they are absolutely perfect! Thank you, thank you! I am in awe. Sharing this recipe with my co-worker, as well as a gluten-intolerant friend, and anyone else who has struggled with finding the perfect gluten-free baked dessert.

    1. I’m so glad you and your co-worker enjoyed them! So nice of you to make them for a GF friend 🙂 Thanks for the comment!

  7. 5 stars
    These were delicious! I made them a few days ahead for Christmas and kept them refrigerated. They stayed soft and wonderful. Thanks for a great recipe!

  8. Those ads that you receive money for and that keep popping in from the left side almost totally prevent me from reading your recipe and are very irritating. There is no X to get rid of it and another one just pops in anyway. Erin, love your excellent recipes but will not look at any more until those ads are gone. By allowing these you are unwittingly losing readers.

  9. I keep flax seeds on hand, but not chia. Do you think this would work if I added ~50% more ground flax? Also, do you measure the seeds before grinding, or is that 2T of chia powder?

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