Gluten-Free Pumpkin Whoopie Pies (With Secret Ingredient Filling!)

Nothing says autumn quite like the warm, spicy aroma of pumpkin treats filling the kitchen. If you’re gluten-free, though, finding those comforting seasonal desserts can be tricky. That’s where these Gluten-Free Pumpkin Whoopie Pies come in—moist, cakey cookies packed with pumpkin spice, sandwiching a creamy, irresistible filling that includes a surprising secret ingredient! Whether you’re making them for a holiday gathering or a cozy afternoon at home, these treats will delight everyone—gluten-free or not.

What Makes These Whoopie Pies Special?

While traditional whoopie pies usually feature a vanilla or marshmallow cream filling, we’ve upgraded the filling with a secret ingredient: Greek yogurt! It might sound unusual, but the Greek yogurt adds a rich, tangy flavor that perfectly balances the sweetness of the cookies, while also providing a creamy texture. Plus, it’s a lighter and healthier twist on the classic recipe.

Why Gluten-Free?

With an increasing number of people opting for gluten-free diets due to celiac disease, gluten sensitivities, or simply for personal health reasons, it’s crucial to find delicious alternatives to your favorite treats. These gluten-free pumpkin whoopie pies don’t sacrifice flavor or texture. They’re moist, fluffy, and bursting with fall spices. Using a gluten-free flour blend ensures that everyone can enjoy these classic autumn desserts without feeling left out.

Ingredients for Gluten-Free Pumpkin Whoopie Pies

To create the perfect whoopie pies, you’ll need high-quality ingredients that come together for a seamless gluten-free experience. Here’s what you’ll need:

For the Pumpkin Cookies:

  • 1 ¾ cups gluten-free all-purpose flour (ensure it has xanthan gum or add ½ tsp if your blend doesn’t)
  • 1 tsp baking powder
  • 1 tsp baking soda
  • ½ tsp salt
  • 1 tsp cinnamon
  • ½ tsp ground ginger
  • ¼ tsp ground cloves
  • ¼ tsp ground nutmeg
  • ¾ cup pumpkin puree (not pumpkin pie filling)
  • ½ cup brown sugar, packed
  • ½ cup granulated sugar
  • ½ cup vegetable oil (or melted coconut oil for a healthier alternative)
  • 1 large egg
  • 1 tsp vanilla extract

For the Secret Ingredient Filling:

  • ½ cup Greek yogurt (plain or vanilla for extra sweetness)
  • 4 oz cream cheese, softened
  • 1 cup powdered sugar
  • 1 tsp vanilla extract
  • 1-2 tbsp maple syrup (optional, for added sweetness)

Step-by-Step Instructions for Making Pumpkin Whoopie Pies

Preparing the Cookies

  1. Preheat your oven to 350°F (175°C). Line two baking sheets with parchment paper or silicone baking mats for easy cleanup.
  2. Mix the dry ingredients. In a medium bowl, whisk together the gluten-free flour, baking powder, baking soda, salt, cinnamon, ginger, cloves, and nutmeg. This spice blend creates that unmistakable pumpkin spice flavor we all love.
  3. Blend the wet ingredients. In a large mixing bowl, combine the pumpkin puree, brown sugar, granulated sugar, oil, egg, and vanilla extract. Mix until smooth.
  4. Combine wet and dry ingredients. Gradually stir the dry ingredients into the wet mixture, mixing until well combined. The dough should be thick and slightly sticky.
  5. Scoop the dough. Using a cookie scoop or tablespoon, drop rounded dollops of dough onto the prepared baking sheets, leaving about 2 inches of space between each one. You want the cookies to be uniform in size for perfect pie sandwiches!
  6. Bake. Place the sheets in the oven and bake for 10-12 minutes, or until the cookies are firm to the touch and lightly golden around the edges. Once done, transfer the cookies to a wire rack to cool completely.

Creating the Secret Ingredient Filling

  1. Cream the cream cheese and yogurt. In a medium bowl, beat together the softened cream cheese and Greek yogurt until smooth and fluffy. This creamy base will create a rich yet light filling.
  2. Sweeten the mixture. Add the powdered sugar, vanilla extract, and maple syrup (if using) to the cream mixture. Beat on low until the powdered sugar is incorporated, then increase the speed to high and whip until smooth and airy.
  3. Refrigerate the filling. If the filling seems too soft, you can place it in the refrigerator for 15-20 minutes to firm up slightly. This will make it easier to spread.

Assembling the Whoopie Pies

  1. Match the cookies. Pair the cooled cookies together by size—this will make for the most uniform whoopie pies.
  2. Spread the filling. Using a butter knife or piping bag, spread a generous amount of the filling onto the flat side of one cookie, then sandwich it with its partner. Gently press together to ensure the filling spreads evenly.
  3. Chill (optional). For a firmer texture, place the assembled whoopie pies in the refrigerator for 30 minutes before serving. This step is optional, but it gives the filling a nice consistency.

Tips for Perfect Gluten-Free Pumpkin Whoopie Pies

  • Don’t overmix the batter! Overmixing can lead to dense cookies. Stir just until the ingredients are combined for a soft and fluffy result.
  • Store-bought vs. homemade gluten-free flour blends: If you’re using a store-bought gluten-free flour blend, make sure it contains xanthan gum. This ingredient is essential for providing structure and chew in gluten-free baked goods.
  • Filling variations: Want to switch up the filling? You can replace Greek yogurt with marshmallow fluff for a sweeter, more traditional filling. Or, add a tablespoon of cinnamon for a spiced cream cheese filling!

FAQs

How do I store gluten-free pumpkin whoopie pies?

  • These whoopie pies should be stored in an airtight container in the refrigerator for up to 5 days. For longer storage, freeze them for up to 2 months.

Can I make these whoopie pies dairy-free?

  • Absolutely! Simply swap the cream cheese with a dairy-free alternative and use coconut or almond yogurt in place of the Greek yogurt.

What’s the best gluten-free flour for these whoopie pies?

  • A high-quality gluten-free all-purpose blend that contains xanthan gum works best. You can also create your own blend with rice flour, potato starch, and tapioca starch.

Can I use fresh pumpkin instead of canned?

  • Yes, but make sure to drain the fresh pumpkin puree to remove excess water. Canned pumpkin is thicker and more consistent, which is why it’s typically preferred in baking.

Why do my cookies spread too much?

  • If your cookies are spreading too much, your dough might be too warm or you may have overmixed it. Chilling the dough for 10-15 minutes before baking can help prevent spreading.

Do I need a whoopie pie pan to make these?

  • Not at all! A cookie sheet works perfectly fine. Just use a cookie scoop to ensure your whoopie pies come out even in size.

Conclusion

These Gluten-Free Pumpkin Whoopie Pies are the ultimate fall treat, boasting soft pumpkin-spiced cookies and a unique, tangy-sweet filling that everyone will love. With the added secret ingredient of Greek yogurt, the filling takes on a luxurious, creamy texture with a slightly tangy twist that complements the pumpkin flavor beautifully. Whether you’re hosting a gathering or looking for a cozy dessert to enjoy at home, these whoopie pies are a guarantee

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