These big, fluffy Gluten Free Pumpkin Whoopie Pies are one of my favorite fall treats. These soft pumpkin cookies are filled with frosting or marshmallow fluff. These homemade whoopie pies are full of delicious fall flavors. They are also dairy-free with a nut-free option.

Gluten free pumpkin whoopie pies on a cupcake stand.

I am still testing some new pumpkin recipes this week. This week we are making whoopie pies! And even better, these whoopie pies have a healthier option! I use almond flour to help keep these soft and use no refined sugars. It will definitely help reduce the sugar buzz!

If you love pumpkin as much as I do, you will want to check out all my yummy gluten free pumpkin recipes!

Why Make This Recipe:

  1. Whoopie pies really are one of my favorite desserts. Anytime you sandwich a sweet glaze or frosting in between two soft, and moist cake-like cookies is a good time for me!
  2. I kept these on the healthy side with no refined sugar.
  3. I include both a nut-free option for those who have a nut allergy.
  4. I use simple, easy-to-find ingredients that also are dairy-free.
  5. You can make these whoopie pies ahead, then fill and assemble them later when you need them.

If you are like me and you feel the need to hide veggies in other desserts, check out these Paleo Delicata Squash Brownies or this Kabocha Squash Mousse.

Top Pick
King Arthur, Measure for Measure Flour 3 lbs

This is one of my favorite gluten-free flour blends for cookies, cakes, pie crust, biscuits, and muffins! (Do not use this flour blend for yeast recipes.)

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Ingredient Notes:

Photos of the pumpkin ingredients for these cookies.
Note almond flour isn’t pictured
  • Gluten Free Flour Blend – I tested this recipe using Bob’s Red Mill 1 to 1 Gluten Free Flour Blend and King Arthur’s Measure for Measure Gluten Free Blend. That doesn’t mean others will not work; I just have not tested other flours, and I can not guarantee the recipe will work if you use different mixes.
  • Almond Flour – I prefer almond flour to almond meal because it is a finer grind. Anthony’s Almond Flour is one of my favorites, and it is very reasonably priced.
  • Baking Powder – I always recommend using aluminum-free to avoid a bitter aftertaste.
  • Pure Vanilla Extract – I do not recommend imitation vanilla. You can check to see if vanilla extract is gluten free.
  • Pumpkin Puree – Canned is best because it is silky and smooth. Do not use pumpkin pie filling.
  • Coconut Sugar – You can substitute brown sugar if you don’t have coconut sugar on hand. Be sure to check to ensure your coconut sugar is gluten free.
  • Coconut Oil – If you prefer, you can also use butter or another cooking oil.
  • Eggs – Use size large.

If these whoopie pies sound good, wait until you try these Gluten Free Chocolate Pumpkin Swirl Muffins!

Recipe Step-By-Step Directions:

You will be surprised by the ingredients used in this recipe. Believe it or not, they are pretty healthy…except for the filling. These pumpkin whoopie pies are soft and melt in your mouth with a delicious hint of pumpkin spice.

A photo of whisking dry ingredients.

Step 1: Preheat the oven to 350º F. Add the dry ingredients to a large mixing bowl. Whisk the ingredients until thoroughly blended.

Whisking wet ingredients together.

Step 2: Add your wet ingredients to a medium-sized bowl and whisk to blend.

Mixing the wet and dry ingredients together.

Step 3: Pour the wet ingredients into the dry ingredients. Mix them into a soft cookie batter.

Gluten free pumpkin cookie dough balls ready to bake on a baking sheet.

Step 4: Use a cookie scoop to drop the batter onto a prepared baking sheet. Using a cookie scoop helps you make cookies roughly the same size so that your bottom and top halves match in size.

The whoopie pies ready to bake.

Step 5: Use your hand or glass and smusg down the cookies a bit. This will ensure your cookies aren’t too tall and will fit in your mouth :-). Bake at 350º F for 9-10 minutes until done.

The actual baking time will depend on the size of your cookies.

Filling whoopie pies with vanilla frosting.

Grab this deliciously easy vanilla frosting recipe. See below for more filling ideas.

Step 6: Use a piping bag filled with vanilla frosting to pipe the frosting onto the whoopie pies. Add a top cookie, and enjoy!

If you love whoopie pies, you will also want to try my chocolate Gluten Free Whoopie Pies recipe.

Two gluten free pumpkin whoopie pies stacked on top of each other.

Filling Ideas:

The whoopie pie cream I used is the frosting that I bought, but you can fill yours with several delicious fillings.

  • Whipped Cream
  • Marshmallow Fluff
  • Frosting

Recipe FAQ:

Can you make these pumpkin whoopie pies nut-free?

Omit the almond flour and add ⅔ cup additional gluten free flour blend.

How do you know when the whoopie pies are finished baking?

You will know these cookies are done because they will be soft but firm to the touch.

How do you store gluten free pumpkin whoopie pies?

These cookies will keep fresh for up to 4 days in an airtight container or for up to 4 months in the freezer.

Can you freeze these whoopie pies?

Yes, you can easily freeze these whoopie pies. I store them in a large Ziplock freezer bag.

two pumpkin whoopie pies stacked on a white stand.

Gluten Free Pumpkin Whoopie Pies

Sandi Gaertner
Gluten free pumpkin whoopie pies are a classic fall treat in our house. Added almond meal helps balance out the sugars, and maple syrup and coconut sugar sweeten these cookies, making them healthier.
Love this recipe?Give it a star rating!
5 from 4 votes
dairy free allergen icon
gluten free allergy icon
soy free allergy icon
vegetarian icon
Prep Time 15 minutes
Cook Time 10 minutes
Total Time 25 minutes
Course Gluten Free Cookies and Bar Recipes, Gluten Free Dessert Recipes
Cuisine American
Servings 10 whoopie pies
Calories 256 kcal

*As an Amazon Associate, I earn a small commission from qualifying purchases.


  • 1 cup gluten free flour blend *see note
  • 1 cup almond flour *see note
  • 1 teaspoon ground cinnamon
  • 1 teaspoon pure vanilla extract
  • 2 teaspoons pumpkin pie spice
  • ½ teaspoon baking soda
  • 1 teaspoon baking powder aluminum-free
  • ½ cup pumpkin puree
  • 2 large eggs
  • ¾ cup coconut sugar or brown sugar
  • ½ cup coconut oil or butter
  • 2 tablespoons maple syrup
  • dash salt


  • Preheat the oven to 350º F.
  • Prepare your baking sheet by either using parchment paper or spray coconut oil on a baking sheet.
  • In a large bowl, add all of the dry ingredients, and whisk to blend.
  • In a small bowl, add all of the wet ingredients (egg, pumpkin, vanilla, and coconut oil) and mix well.
  • Pour the wet ingredients into the dry ingredients and mix.
  • Use a cookie scoop to drop dough onto the baking sheet.
  • Use a clean hand or the bottom of a glass to flatten and shape, so all of the cookies are the same size.
  • Bake 10 minutes until done.
  • When the cookies are cool, add frosting to one cookie and put another cookie on top to make a sandwich.


  1. I have tested this recipe with King Arthur Measure for Measure GF, Bob’s Red Mill 1 to 1 GF blend, and Authentic Foods Multi Blend in this recipe. That doesn’t mean others will not work, I just have not tested other flours.
  2. If your gluten free flour blend doesn’t contain Xanthan Gum or Guar Gum, please add 1 teaspoon.
  3. Note, you can substitute brown sugar for coconut sugar and butter instead of coconut oil.


Please know that every gluten free flour blend has a different starch to grain ratio. If you use a blend I didn’t test, you may need to adjust your moisture levels in your baked goods.


Serving: 1gCalories: 256kcalCarbohydrates: 23gProtein: 5gFat: 18gSaturated Fat: 10gCholesterol: 33mgSodium: 92mgPotassium: 78mgFiber: 3gSugar: 9gVitamin A: 1954IUVitamin C: 1mgCalcium: 62mgIron: 1mg
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Nutrition Disclaimer

Nutritional information is an estimate provided to you as a courtesy. You should calculate the actual nutritional information with the products and brands you are using with your preferred nutritional calculator.

This post was updated from the original 11/14 post with more details and tips.

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    1. Hi Lynn, almond flour by itself will not work in gluten free baking. You need to add starch and a binder so they hold together. I haven not tested my recipe with just almond flour.

      1. Hi Kristina, To make these nut-free, omit the almond flour and add 1/2 cup additional flour. You may need to adjust the flour ratio slightly depending on the gluten free blend you are using.

  1. I have never made whoopie pies, but I can’t wait to try this recipe when we are back at home! Thank you so much for sharing this post at the Hearth and Soul Link Party, Sandi. I really appreciate it, Sandi! Pinning of course, and I’m featuring it at this week’s H&S.

  2. I made this for my ceriac friend for morning tea, because she always miss out baking goods when we gather for meetings. She absolutely loved it.

  3. I love pumpkin whoopie pies! Edna’s makes a great one which I am usually able to get if I’m early enough at the Mtn View Farmer’s market (which moves to Palo Alto on 49ers home game days).

    I’ll have to try this recipe and too have not bought the TJ’s pumpkin caramel sauce so we shall see if I get lucky. I did buy 6 boxes of their gluten free pumpkin pancake mix which is fantastic. Can’t find it anywhere now 🙁

    1. I am so jealous. I didn’t realize how good the Trader Joe’s gluten free pumpkin pancake mix was….until it was gone within a week 🙂 Definitely grab the pumpkin caramel. The Trader Joe’s in Los Gatos is down to 2 jars as of yesterday.

      I also like Edna’s. They are at our Campbell farmer’s market as well.

  4. I’ve made classic whoopee pies gluten free, but not pumpkin ones. Sandi, these look great! I’m so jealous of all of you who have a TJ’s nearby. Pumpkin Caramel Sauce … I want some of that! For this recipe and many others or just for spreading on something or eating a little with a spoon. 😉


      1. You are too sweet, Sandi! We have one about 90 minutes away. I’ll ask a friend if she wants to pick up some for me. 😉 That would be easier than you shipping it to me! But thank so much for the super generous offer!


  5. Gluten Free Pumpkin Whoopie Pies sound like something I would love! I can’t wait to make this

  6. These look so yummy! I saw that pumpkin caramel sauce last week at Trader Joe’s and am now kicking myself in the butt for not getting it because now it’s popping up everywhere!

  7. The gluten free Pumpkin Whoopie Pies are delicious………! I love them, I’m obsessed with using pumpkin this year. Thanks for sharing a delicious sweet treat.

  8. In my wildest dreams, I cannot imagine being able to make gluten-free whoopie pies! I’m excited to make these for the holidays for my family friends who cannot have gluten. Thank you!

    1. I hope your friends enjoy these Linda. It is really kind of you to want to make a special treat for your gluten free friends 🙂