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Gluten Free Pumpkin Spice Whoopie Pies

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These Gluten Free Pumpkin Spice Whoopie Pies are made with an oat and almond flour blend, coconut sugar, and plenty of pumpkin and spice.  The whoopie pies are soft, perfectly sweet, filled with a velvety maple cinnamon cream cheese frosting, and are the ideal fall dessert!

Two gluten free pumpkin spice whoopie pies stacked on a plate.

Gluten Free Pumpkin Whoopie Pies

This pumpkin whoopie recipe is adapted from my original pumpkin spice whoopie pies recipe.  And just like the original, the gluten free version packs the same amount of flavor with plenty of pumpkin, fall spices, and an eat-by-the-spoonful filling.

Even though these spiced pumpkin whoopie pies are gluten free, you will be hard-pressed to tell the difference.  

here’s What to expect when you make the whoopie pies:

  • An easy recipe – Two bowls, no mixer, and a cookie scoop is all you need!
  • Small batch serving – The recipe yields 4 generously sized whoopie pies.  However, you can make a few more by making your whoopie pies smaller.
  • Remarkably soft – The whoopie pies are soft like cake, but sturdy like a cookie.  Two things you want with a handheld dessert!
  • Perfectly sweet – You will get plenty of pure sweetness with the coconut sugar.  Plus, the maple syrup adds a delicious buttery caramel note.
  • Lots of flavor – This dessert screams fall with the pure pumpkin and pumpkin pie spice.
Filled pumpkin whoopie pies arranged on a wood cutting board.

What exactly is a whoopie pie?

You may be even more curious about that, than what the whoopie pie will taste like!  I think it all depends on who you ask, but some consider it a cookie, while others consider it a cake.   But, at the end of the day, the whoopie pie is two soft baked and flavored rounds with a filling sandwiched in the middle.

I tend to think of the whoopie pie as a soft baked cookie sandwich because the whoopie pie is denser than a cake.  It is still soft and moist, but I’m pretty sure if I served up a slice of a whoopie pie batter as a cake, I’d get feedback that it is way too dense.

Additionally, because it is a handheld and sturdy dessert, I lean more towards cookie.  And a versatile cookie at that!  You can make the whoopie pies in a variety of flavors – like my chocolate mint whoopie pies for example.  And you can fill them with just about any frosting or filling you like!

Small Batch Dessert For Fall

Obviously, I like making small batch desserts!  However, I like making small batch holiday desserts even more.  When fall rolls around, I immediately start thinking about all the sweet treats I want to make.  And with the small portion recipes, I can make a tasty variety without tons of leftovers.

Just think of all the fall desserts that can make up a beautiful sampler table:  these delightful gluten free pumpkin whoopie pies, cinnamon sugar pumpkin bread, a mesmerizing pumpkin roll cake, gluten free apple spice cupcakes, pumpkin spice sugar cookies, and gluten free mini pumpkin pie!  If I see that menu lineup on a holiday gathering invite, I’m in!

Everything You Will Need To Make These Pumpkin Spice Whoopie Pies

dry Ingredients

  • Oat Flour – The oat flour makes the whoopie pies lighter and softer.  You can purchase oat flour, or make your own by grinding up gluten free rolled oats into flour (which is what I do).
  • Almond Flour – The almond flour adds flavor, moisture, and texture.  I recommend blanched superfine almond flour.   
  • Sweet Rice Flour – Sweet rice flour provides structure in that it’s properties mimic gluten.  It also provides moisture.  When baking with sweet rice flour, I will always recommend allowing the batter to rest for a few minutes before baking, so the sweet rice flour can bind with the other ingredients and the batter can hydrate.  
  • Tapioca Flour – Also referred to as tapioca starch.  The tapioca flour adds texture and chew.
  • Pumpkin Pie Spice – I like to keep it easy and use pre-made pumpkin pie spice to make my pumpkin spice whoopie pies!
  • Baking Powder and Baking Soda – Both will aid in texture and rise.  I find that with some gluten free baking, both are needed to give the baked good a little help rising.
  • Salt – Salt is a wonderful flavor enhancer!

Wet Ingredients

  • Coconut Sugar – Coconut sugar not refined like regular sugar, and offers a delicate sweetness with caramel notes.  You can substitute granulated sugar if you prefer.
  • Maple Syrup – Another refined free sugar, the maple syrup will add moisture along with a sweet buttery flavor.
  • Egg Yolk – Only 1 egg yolk is all we need!
  • Sour Cream – The sour cream helps the whoopie pies to stay soft and moist without thinning out the batter.
  • Coconut Oil – The coconut oil provides fat to the batter.  It can be replaced with melted butter.
  • Vanilla Extract – Flavor!

Baking Equipment

  • Mixing Bowls
  • Baking Sheet – A standard size baking sheet that is lined with parchment paper.
  • Cookie Scoop – I like to use a medium cookie scoop to easily measure out the batter.
Gluten free pumpkin spice whoopie pies arranged in a pair in a small white dish.

Helpful Baking Tips

  1. Bring all of the refrigerated ingredients to room temperature – When all of the ingredients start at the same temperature, they will mix and bake more evenly.
  2. Whisk the dry ingredients together first – I prefer to whisk the dry ingredients together first so they get mixed evenly and are free of lumps.
  3. Use pure pumpkin – not pumpkin pie filling – Pure pumpkin is just that, only pumpkin.  While pumpkin pie filling has a lot of added ingredients we don’t need (or want).
  4. Let the batter rest before baking – I said it before, but it bears repeating.  The batter needs a little time to hydrate to bake with proper structure.
  5. Use a cookie scoop to portion your batter – The number 1 reason for this is that the scoop makes portioning the whoopie pie batter so much easier.
  6. Let the whoopie pies cool completely before filling – For the obvious reason – the filling will melt out of your pumpkin whoopie pies if you assemble the whoopie pies while they are still warm!

What To Make With The Leftover Pumpkin

You will have leftover pumpkin.  Which, for this time of year isn’t a bad thing!  You can bake another batch of pumpkin spice whoopie pies, or browse all of my pumpkin recipes.  Below are some of my favorites for using leftover pumpkin:

A stack of three pumpkin spice whoopie pies on a small wooden plate.

FAQ’s for the gluten free pumpkin whoopie pies

Can this recipe be doubled?

I have not tested a larger batch. But if you do, please let me know how they turn out!

Will a 1:1 gluten free flour blend work instead of your flour blend?

Probably not. Not all gluten free flours are the same. I find the 1:1 blends to yield a much drier bake, and a lot of the ingredient ratios would probably need to be adjusted.

Does oat flour have gluten?

No. Oats are naturally gluten free. However, depending on the brand, there could be the possibility of cross-contamination with other products processed. I recommend looking for a brand that has the gluten free label to ensure there was no cross-contamination.

Can I make the whoopie pies vegan/dairy free?

I can’t say for certain as I have only tested the recipe as written. If you do, let me know!

Are whoopie pies supposed to be sticky?

Yes. All of that moisture in the whoopie pie is inherently going to make them a little sticky. And the longer they sit out, the stickier they may get. I refrigerate my whoopie pies to preserve the filling and reduce the stickiness.

Can I freeze the whoopie pies?

You can freeze un-filled whoopie pies for up to 3 months. I would individually wrap them and put in a Ziploc bag, then defrost in the refrigerator. I do not recommend freezing the maple cinnamon cream cheese frosting because the fat content in the frosting may cause it to separate when thawed.

Two gluten free pumpkin spice whoopie pies set in a pretty white baking dish.
Two gluten free pumpkin spice whoopie pies stacked on a plate.
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5 from 2 reviews

Gluten Free Pumpkin Spice Whoopie Pies

Yield: 4 Whoopie Pies
These Gluten Free Pumpkin Spice Whoopie Pies are made with an oat and almond flour blend, and plenty of pumpkin and spice.  The whoopie pies are soft, perfectly sweet, filled with a velvety maple cinnamon cream cheese frosting, and are the ideal fall dessert!
Prep15 minutes
Cook14 minutes
Total29 minutes


Cinnamon Maple Cream Cheese Frosting

  • 2 ounces cream cheese, room temperature
  • 2 tablespoons pure maple syrup
  • 1/4 cup heavy cream
  • 1 tablespoon powdered sugar
  • 1/2 teaspoon ground cinnamon
  • 1/8 teaspoon salt

Pumpkin Spice Whoopie Pies


Cinnamon Maple Cream Cheese Frosting

  • The Cinnamon Maple Cream Cheese Frosting can be made in advance and refrigerated, or while the whoopie pies are baking and cooling. See the link to the separate recipe post for the frosting for more tips and FAQ's!
  • In a small mixing bowl, add the cream cheese and maple syrup. Use a hand held mixer on medium speed to beat the cream cheese until it is smooth and creamy.
    2 ounces cream cheese, room temperature, 2 tablespoons pure maple syrup
  • Add the heavy cream, powdered sugar, cinnamon, and salt. Continue to beat on medium high speed until light and fluffy. This may take about 2 minutes. Do not overmix, or the frosting may separate. Note – If you prefer a much thicker frosting, add more powdered sugar 1 tablespoon at a time until you reach your desired consistency.
    1/4 cup heavy cream, 1 tablespoon powdered sugar, 1/2 teaspoon ground cinnamon, 1/8 teaspoon salt
  • The frosting is ready to use immediately, or it can be covered and refrigerated where it will thicken as it chills. 

Pumpkin Spice Whoopie Pies

  • Preheat oven to 350F degrees and adjust the oven rack to the middle position. Line a baking sheet with a piece of parchment paper.
  • In a small mixing bowl, whisk together the oat flour, almond flour, sweet rice flour, tapioca flour, baking powder, baking soda, salt, and pumpkin pie spice.
    6 tablespoons gluten free oat flour, 3 tablespoons blanched almond flour, 2 tablespoons sweet rice flour, 2 tablespoons tapioca flour, 1/4 teaspoon baking powder, 1/8 teaspoon baking soda, 1/8 teaspoon salt, 1 teaspoon pumpkin pie spice
  • In a medium mixing bowl, add the sugar, maple syrup, egg yolk, sour cream, oil, pumpkin puree, and vanilla extract. Whisk until blended and smooth. Sprinkle half of the dry ingredients over the wet ingredients and stir until just incorporated. Then sprinkle in the remaining dry ingredients and mix until no dry streaks remain.
    1/4 cup organic cane sugar, 2 tablespoons pure maple syrup, 1 large egg yolk, room temperature, 3 tablespoons full fat sour cream, room temperature, 2 tablespoons cold pressed refined coconut oil, melted, 1/4 cup + 1 tablespoons pure canned pumpkin, 1/2 teaspoon vanilla extract
  • Let the batter rest for at least 5 minutes – this allows the gluten free flours to hydrate.
  • Using a cookie scoop scoop 8 equal portions of the batter onto the prepared baking sheet – at least 2 inches apart. Note – I use a cookie scoop that holds approximately 2 tablespoons of batter.
  • Bake for 12 to 14 minutes, or until the tops of the cookies are set and spring back when gently touched with your finger. Cool the cookies on the baking sheet set on wire cooling rack for 5 minutes. Then transfer the cookies to the wire rack to cool completely.
  • Dollop equal portions of the frosting on half of the pies, assemble, and Enjoy!
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  • Oat Flour – You can purchase oat flour, or grind gluten free rolled oats into flour in a food processor or blender.
  • Pumpkin – Depending on the brand, canned pumpkin can have different names, but is the same thing:  Pumpkin Puree, Pure Pumpkin, 100% Pumpkin, Organic Pure Pumpkin.  Just be sure it is not Pumpkin Pie Filling
  • Leftover Pumpkin – You will have leftover pumpkin, regardless of the size can you use.  Check out my other pumpkin recipes to make another batch of pumpkin treats!
  • Storing Leftovers – I recommend storing the whoopie pies covered in the refrigerator because of the dairy in the filling.
  • Substitutions – I have only tested the recipe as written.  The cane sugar is easily swapped 1:1 with coconut sugar or granulated sugar.
Course: Dessert
Cuisine: American
Author: Erin Cernich


Calories: 414kcal | Carbohydrates: 47g | Protein: 5g | Fat: 24g | Saturated Fat: 14g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 4g | Cholesterol: 82mg | Sodium: 265mg | Potassium: 186mg | Fiber: 2g | Sugar: 29g | Vitamin A: 3405IU | Vitamin C: 1mg | Calcium: 105mg | Iron: 1mg
Nutrition information is calculated by a third-party and should only be considered an estimate and not a guarantee.
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about the author ...

I'm Erin and I'm all about desserts - and a little bit of butter!

I've tested, written, and photographed hundreds of recipes on my website. Here you'll find the tastiest small batch desserts - all homemade, all simple, and all for you! Click here to learn more about me!

5 from 2 votes (2 ratings without comment)

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