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These mini pumpkin whoopie pies with marshmallow filling taste like a mix of pumpkin cake and cookie, filled with fluffy marshmallow for an easy fall treat.
Chocolate whoopie pies can wait.
This fall is all about pumpkin mini whoopie pies!
These pumpkin desserts are the perfect addition to the holiday table, especially when you want something that serves easily, comes together effortlessly, and is guaranteed to please the crowd.

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Pumpkin is a classic choice for Thanksgiving dessert ideas. Beyond whoopie pies, our Libbyโs pumpkin pie and pumpkin bread with cream cheese are perfect for sharing!
Why You’ll Love This Mini Pumpkin Whoopie Pies with Marshmallow Filling Recipe
- These mini pumpkin whoopie pies with marshmallow filling are single-serve and portable, perfect for parties and on-the-go snacking!
- These pumpkin whoopie pies with marshmallow filling are make-ahead friendly and hold up beautifully until ready to serve.
- These small batch pumpkin whoopie pies are soft, deliciously spiced, and prepared for any filling you love.
Ingredients
Pumpkin spice whoopie pies:
All-purpose flour – We havenโt tested other kinds of flour in this whoopie pie recipe with marshmallow fluff, so itโs best to stick with good old all-purpose flour.
Baking soda and baking powder – Leaveners to help the pumpkin cookies rise perfectly.
Salt and vanilla extract – They help bring out the flavors in these mini pumpkin whoopie pies with marshmallow filling.
Ground cinnamon, ground cloves, ground ginger, and ground allspice – These individual pumpkin pies wouldnโt feel right without the cozy blend of pumpkin pie spices.
Light brown sugar – The deep, caramel-like sweetness of brown sugar matches beautifully with the pumpkin spice flavor of this pumpkin whoopie pie recipe.
Vegetable oil – For moist cookies!
Canned pumpkin puree – You can make your own pumpkin puree, but the canned version saves time.
Eggs – For the pumpkin cookies’ structure and texture. Be sure to use room-temperature eggs for easy mixing!
Marshmallow filling:
Unsalted butter and confectionersโ sugar – The rich base of our marshmallow filling.
Marshmallow fluff – You can use store-bought or homemade.
Vanilla extract – The classic flavor that rounds out the marshmallow filling.
Ingredient Substitutions For Mini Pumpkin Whoopie Pies
Natural maple extract
Try pumpkin whoopie pies with maple filling by swapping the vanilla for maple extract in the marshmallow fluff.
Cinnamon buttercream filling
Pumpkin whoopie pies with buttercream are just as tasty as the marshmallow fluff version, especially when the buttercream is mixed with a little ground cinnamon.
Maple cream cheese filling
Make pumpkin whoopie pies with cream cheese filling by whipping together 3 cups of powdered sugar, 8 ounces of softened cream cheese, 1/2 cup softened salted butter, 1 teaspoon vanilla extract, and 3 tablespoons of maple syrup for a decadent fall frosting.
Tips For Making This Recipe
Ensure Soft Cookies
For perfectly soft mini pumpkin whoopie pies with marshmallow filling, measure the flour properly and do not overmix the cookie batter!
Allow the Cookies to Cool
Let the pumpkin cookies cool completely before assembly, or the marshmallow filling will melt and make a mess. For the best flavor and texture, refrigerate the mini pumpkin whoopie pies for at least 30 minutes before serving.
Make Your Own Marshmallow Fluff
Did you know itโs easy to make your own marshmallow fluff with just marshmallows and corn syrup? Youโll find the instructions in this post’s FAQ section!
Pumpkin Whoopie Pies with Marshmallow Filling FAQs
What is a whoopie pie?
A whoopie pie is a dessert made with two cake-like cookies sandwiched together with a creamy filling.
How to make homemade marshmallow fluff?
You can make your own marshmallow fluff for these small-batch pumpkin whoopie pies! Melt about 20 marshmallows over low heat in a double boiler, then stir in 2 teaspoons of corn syrup once the marshmallows are sticky. Keep stirring until the mixture is smooth and lump-free!
How to keep whoopie pies from getting sticky?
Donโt forget to line your baking sheets with parchment paper and let the pumpkin cookies cool before handling. Since these pumpkin mini whoopie pies can get sticky on the counter, itโs also best to store them in the fridge.
Do you refrigerate whoopie pies?
Yes! Refrigerate your mini whoopie pies to maintain their texture. Theyโll keep in an airtight container in the fridge for up to 3 days, perfect for prepping in advance.
Can I freeze pumpkin whoopie pies?
Absolutely! Wrap each pumpkin whoopie pie in foil, keep them in a freezer-safe bag, and store for 2 to 3 months. Thaw the frozen pumpkin pie whoopie pies at room temperature before serving.
More Delicious Pumpkin Treats
I found this recipe for Pumpkin Brownies that I HAVE to try!
Yay! You have made it this far, and I am so glad! Hey โ If you make this recipe, Iโd love for you to give it a quick review & star rating โ below.
Mini Pumpkin Whoopie Pies
Ingredients
For the pumpkin whoopie pies:
- 3 cups all-purpose flour
- 1 tsp baking soda
- 1 tsp baking powder
- 1 tsp salt
- 2 tbsp ground cinnamon
- 1 tsp ground cloves
- 1 tsp ground ginger
- 1 tsp ground allspice
- 2 cups light brown sugar, packed
- 1 cup vegetable oil
- 2 1/2 cups pumpkin puree
- 2 large eggs, room temperature
- 1 tbsp vanilla extract
For the marshmallow filling:
- 1 stick unsalted butter, room temperature
- 1 1/4 cups confectionersโ sugar
- 2 cups marshmallow fluff
- 1 tbsp vanilla extract
Instructions
- Gather the ingredients.
- Preheat the oven to 350ยฐF and line your baking sheets with parchment paper.
- Whisk the dry ingredients together until combined.
- In another bowl, mix the brown sugar and oil. Whisk in the pumpkin puree.
- Add the eggs and vanilla extract to the pumpkin mixture and mix until incorporated.
- Add the flour mixture to the wet ingredients, half a cup at a time, until a dough forms.
- Portion the dough with a tablespoon and drop it onto the prepared baking sheets, about an inch apart.
- Bake the cookies for 15 minutes.
- Let the cookies cool on the baking sheet for 10 minutes, then transfer them to a wire rack to cool completely.
- Beat the marshmallow filling ingredients together on medium speed for 3 minutes or until smooth.
- Spread a tablespoon of marshmallow fluff filling on the flat side of one cookie, then top with another cookie.
- Repeat with the remaining cookies and filling.
Notes
- For perfectly soft mini pumpkin whoopie pies with marshmallow filling, measure the flour properly and do not overmix the cookie batter!
- Let the pumpkin cookies cool completely before assembly, or the marshmallow filling will melt and make a mess. For the best flavor and texture, refrigerate the mini pumpkin whoopie pies for at least 30 minutes before serving.
- Did you know itโs easy to make your own marshmallow fluff with just marshmallows and corn syrup? Youโll find the instructions in this post’s FAQ section!
Nutrition
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