Mini Pumpkin Whoopie Pies with Marshmallow Filling

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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.

pumpkin whoopie pies

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Pumpkin is a classic choice for Thanksgiving dessert ideas. Beyond whoopie pies, our Libbyโ€™s 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.
Mini Pumpkin Whoopie Pies with Marshmallow Filling

Ingredients

Pumpkin spice whoopie pies:

All-purpose flour We havenโ€™t tested other kinds of flour in this whoopie pie recipe with marshmallow fluff, so itโ€™s best to stick with good old all-purpose flour.

Baking soda and baking powderLeaveners to help the pumpkin cookies rise perfectly.

Salt and vanilla extractThey help bring out the flavors in these mini pumpkin whoopie pies with marshmallow filling.

Ground cinnamon, ground cloves, ground ginger, and ground allspiceThese individual pumpkin pies wouldnโ€™t feel right without the cozy blend of pumpkin pie spices.

Light brown sugarThe deep, caramel-like sweetness of brown sugar matches beautifully with the pumpkin spice flavor of this pumpkin whoopie pie recipe.

Vegetable oilFor moist cookies!

Canned pumpkin pureeYou can make your own pumpkin puree, but the canned version saves time.

EggsFor the pumpkin cookies’ structure and texture. Be sure to use room-temperature eggs for easy mixing!

Marshmallow filling:

Unsalted butter and confectionersโ€™ sugarThe rich base of our marshmallow filling.

Marshmallow fluffYou can use store-bought or homemade.

Vanilla extractThe classic flavor that rounds out the marshmallow filling.

mini pumpkin whoopie pies ingredients

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 itโ€™s easy to make your own marshmallow fluff with just marshmallows and corn syrup? Youโ€™ll find the instructions in this post’s FAQ section!

What Are Pumpkin Whoopie Pies

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?

Donโ€™t 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, itโ€™s also best to store them in the fridge.

Do you refrigerate whoopie pies?

Yes! Refrigerate your mini whoopie pies to maintain their texture. Theyโ€™ll 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.

What Do Mini Pumpkin Whoopie Pies Taste Like

More Delicious Pumpkin Treats

I found this recipe for Pumpkin Brownies that I HAVE to try!

mini pumpkin whoopie pies

Yay! You have made it this far, and I am so glad! Hey โ€“ If you make this recipe, Iโ€™d love for you to give it a quick review & star rating โ˜… below.

mini pumpkin whoopie pies with marshmallow filling

Mini Pumpkin Whoopie Pies

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.
Print Pin Rate
Course: Desserts
Cuisine: American
Keyword: mini pumpkin whoopie pies with marshmallow filling
Prep Time: 10 minutes
Cook Time: 15 minutes
Additional Time: 10 minutes
Total Time: 35 minutes
Servings: 30 mini pies
Calories: 255kcal
Author: Louisa

Ingredients

For the pumpkin whoopie pies:

For the marshmallow filling:

Instructions

  • Gather the ingredients.
  • Preheat the oven to 350ยฐF and line your baking sheets with parchment paper.
  • Whisk the dry ingredients together until combined.
    step 3b mini pumpkin whoopie pies
  • In another bowl, mix the brown sugar and oil. Whisk in the pumpkin puree.
    step 4b mini pumpkin whoopie pies
  • Add the eggs and vanilla extract to the pumpkin mixture and mix until incorporated.
    step 5 mini pumpkin whoopie pies
  • Add the flour mixture to the wet ingredients, half a cup at a time, until a dough forms.
    step 6a mini pumpkin whoopie pies
  • Portion the dough with a tablespoon and drop it onto the prepared baking sheets, about an inch apart.
    step 7 mini pumpkin whoopie pies
  • 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.
    step 9 mini pumpkin whoopie pies
  • Beat the marshmallow filling ingredients together on medium speed for 3 minutes or until smooth.
    step 10a mini pumpkin whoopie pies
  • Spread a tablespoon of marshmallow fluff filling on the flat side of one cookie, then top with another cookie.
    step 11a mini pumpkin whoopie pies
  • 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 itโ€™s easy to make your own marshmallow fluff with just marshmallows and corn syrup? Youโ€™ll find the instructions in this post’s FAQ section!
*This recipe was originally published on 11/2010 by Jaclyn. Notes and photos were updated on 9/2025.

Nutrition

Serving: 1g | Calories: 255kcal | Carbohydrates: 39g | Protein: 2g | Fat: 11g | Saturated Fat: 3g | Polyunsaturated Fat: 4g | Monounsaturated Fat: 3g | Trans Fat: 0.2g | Cholesterol: 21mg | Sodium: 73mg | Potassium: 89mg | Fiber: 1g | Sugar: 25g | Vitamin A: 3292IU | Vitamin C: 1mg | Calcium: 37mg | Iron: 1mg

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Mini Pumpkin Whoopie Pies with Marshmallow Filling
Mini Pumpkin Whoopie Pies

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