Ultimate Gluten-Free Pumpkin Whoopie Pies: Your New Favorite Fall Dessert

Prepare to fall in love with autumn all over again with our incredible Gluten-Free Pumpkin Whoopie Pies recipe. This isn’t just any fall treat; it’s a perfectly balanced masterpiece featuring fluffy, cake-like pumpkin cookies embracing a rich, creamy, and undeniably luscious cream cheese filling. The secret ingredient in our frosting elevates this dessert from delightful to absolutely unforgettable, making it a must-try for any pumpkin enthusiast or gluten-free baker.

As the days grow shorter and the air turns crisp, the aroma of pumpkin baking fills kitchens everywhere. While pumpkin spice everything might seem ubiquitous, there’s a good reason for the hype when it comes to truly exceptional pumpkin recipes. Dishes like our comforting Gluten-Free Pumpkin Streusel Bread, satisfying Gluten-Free Pumpkin Bars, or spiced Gluten-Free Pumpkin Snickerdoodles demonstrate just how cozy and deeply satisfying autumn flavors can be. And now, these Gluten-Free Pumpkin Whoopie Pies are joining the ranks of our most beloved seasonal treats.

Imagine: two pillowy-soft, warmly spiced gluten-free pumpkin cookies sandwiching a rich, easy-to-make cream cheese frosting. Doesn’t that sound absolutely delightful? This unique combination promises everything you love about fall desserts: comforting warm spices, a wonderfully fluffy texture that melts in your mouth, and a rich, creamy filling made extraordinary by our special secret ingredient. It’s a dessert that truly captures the essence of the season, offering a fun and exciting alternative to traditional pies for your holiday gatherings, especially if you’re looking for an impressive gluten-free Thanksgiving dessert.

For those new to the world of whoopie pies, these beloved New England confections playfully blur the lines between cake, cookie, and pie. Essentially, a whoopie pie is a delightful sandwich cookie consisting of two soft, cake-like cookies joined together by a generous layer of creamy frosting or filling. Our rendition takes this charming classic and infuses it with the irresistible flavor of pumpkin, all while being completely gluten-free. It’s a wonderfully nostalgic yet fresh way to enjoy your favorite fall flavors.

Ready to embark on a baking adventure that will yield the most enchanting fall dessert? Let’s dive into the simple yet powerful ingredients that make these Gluten-Free Pumpkin Whoopie Pies so special.

How To Make Gluten-Free Pumpkin Whoopie Pies, Step By Step

For exact ingredient quantities, a convenient printable recipe card, and more expert advice, please scroll down to the full recipe card located at the bottom of this page.

Part 1: Crafting the Fluffy Gluten-Free Pumpkin Cookies

The foundation of our irresistible whoopie pies lies in these perfectly soft, moist, and spiced pumpkin cookies. Follow these detailed steps for flawless results every time:

1. Preheat The Oven & Prepare Baking Sheets. Start by accurately preheating your oven to 350°F (175°C). This ensures a consistent baking environment from the moment your cookies enter the oven. Line two standard baking sheets with high-quality parchment paper or, for superior non-stick results and uniform baking, a macaron silicone baking mat (often called a macaron silpat). Have a medium cookie scoop (roughly 2 tablespoons capacity) or a piping bag fitted with a large open round tip ready for neatly portioning the batter.
2. Combine Sugar & Oil for the Wet Base. In a spacious large mixing bowl, combine the measured brown sugar with your chosen neutral oil. Whisk these two ingredients together thoroughly until they are well combined and the mixture takes on the appearance of wet, granulated sand. This initial step helps to partially dissolve the sugar and ensures that moisture is evenly distributed throughout the subsequent batter.
3. Incorporate Remaining Wet Ingredients for Richness. Gradually mix in the unsweetened pumpkin puree until the mixture is smooth and fully blended. Next, add the large eggs one at a time, making sure to mix thoroughly after each addition until each egg is fully incorporated before adding the next. This careful process prevents the batter from separating or becoming lumpy, ensuring a smooth, emulsified consistency. Finally, stir in the pure vanilla extract, which wonderfully enhances the warm pumpkin spices.
4. Gently Fold in Dry Ingredients. In a separate, medium-sized bowl, whisk together the gluten-free flour blend, baking soda, baking powder, kosher salt, and your custom blend of warm spices: ground cinnamon, nutmeg, ginger, and cloves. Whisking them separately ensures these leavening agents and spices are evenly distributed throughout the flour mixture. Add this dry mixture to your wet ingredients. Using a rubber spatula, gently fold the ingredients until they are just combined and no visible streaks of flour remain. It is crucial not to over-mix the batter, as excessive stirring can lead to a tougher, less tender cookie texture, even with gluten-free flour. A few small lumps are preferable to an over-mixed batter.
5. Precisely Portion Out The Cookies. For uniform size and consistent baking, utilize a medium 2-Tablespoon cookie scoop or a piping bag fitted with a large open round tip. Measure out the dough into 1.5-inch rounds, placing them onto the prepared baking sheets. Ensure you space them about 2 inches apart to allow for proper spread during baking. If any portions have slightly rough edges, gently smooth them with a fingertip lightly moistened with water. You should aim for 9-12 cookies per baking sheet, depending on its specific dimensions.
6. Bake to Perfection & Shape if Desired. Bake the pumpkin whoopie pie cookies for approximately 10-12 minutes. The cookies are perfectly baked when the edges are visibly set, the tops gently spring back when lightly pressed, and a toothpick inserted into the center emerges clean or with only a few moist crumbs attached. Be careful not to overbake, as this can lead to dry whoopie pies. Immediately after removing them from the oven, while still hot and pliable, you can optionally use a round cookie cutter (slightly larger than your cookies) to gently coax them into a more perfect circular shape, yielding a professional and uniform appearance.
7. Cool Completely for Best Results. Allow the baked cookies to cool on the baking sheets for 1-2 minutes. This brief cooling period helps them set before they are moved. Then, carefully transfer them to a wire cooling rack to cool completely. It is absolutely essential that the cookies are entirely cool before proceeding to the frosting stage; warm cookies will cause your beautiful cream cheese frosting to melt and make a messy situation. If baking in batches, alternate between your two baking sheets, always placing cool batter onto a cool baking sheet for optimal and consistent baking performance.

Part 2: Whipping Up the Secret-Ingredient Cream Cheese Frosting & Assembly

This luscious cream cheese filling is the crowning glory of our whoopie pies, offering a rich, tangy-sweet counterpoint to the spiced pumpkin cookies. Here’s how to create this delectable frosting and assemble your treats:

1. Cream Butter & Cream Cheese Until Smooth. The key to a flawlessly smooth, lump-free cream cheese frosting begins with ensuring your unsalted butter and full-fat cream cheese are both properly softened to room temperature. If they are too cold, they will not blend harmoniously, resulting in a clumpy texture. In a large mixing bowl, or the bowl of a stand mixer fitted with a paddle attachment, combine the softened cream cheese and butter. Beat them together on medium speed for 1-2 minutes, or until the mixture is light, creamy, and thoroughly combined, scraping down the sides as needed.
2. Gradually Add Powdered Sugar. Reduce the mixer speed to medium-low. Add the powdered sugar into the creamed butter and cheese mixture gradually, about ½ cup at a time. Mix well after each addition until the sugar is fully incorporated. This careful, gradual addition prevents a cloud of sugar from dusting your kitchen and ensures the frosting develops a silky-smooth consistency.
3. Introduce Finishing Touches & The Secret Ingredient. Stop the mixer and use a rubber spatula to thoroughly scrape down the sides and bottom of the bowl, ensuring all ingredients are evenly mixed and no pockets of uncreamed butter or sugar remain. Now, add the vanilla extract, a tiny pinch of salt (typically less than 1/8 teaspoon is sufficient to brighten flavors without making it salty), 1 tablespoon of heavy cream (which adds richness and aids in achieving a perfect consistency), and finally, our beloved secret ingredient: 1-2 tablespoons of either caramel sauce or pure maple syrup.
4. Whip The Frosting to Fluffy Perfection. Increase the mixer speed to medium-high and beat the frosting for an additional 1-3 minutes. This final whipping step is crucial for incorporating air, which transforms the frosting into a wonderfully smooth, light, and fluffy texture. Check the consistency: if your frosting seems too thin for piping or spreading, add powdered sugar 1 tablespoon at a time until it reaches your desired stiffness. Conversely, if it’s too thick, add more heavy cream, 1 teaspoon at a time, until it loosens up to a perfect, spreadable consistency.
5. Assemble Your Whoopie Pies. Once all your pumpkin cookies are completely cooled and your frosting is prepared to perfection, it’s time for the exciting assembly! Flip over half of your baked cookies so that their flat, bottom side faces upwards. These will serve as the base for your delightful cookie sandwiches. Using either a piping bag fitted with your preferred tip or an offset spatula, generously pipe or spread the prepared cream cheese frosting onto the flat side of these base cookies. Then, gently place a second cookie, flat side down, on top of the frosting to complete each whoopie pie sandwich.
6. Store & Serve for Optimal Freshness. For the best flavor and texture, we recommend chilling your assembled Gluten-Free Pumpkin Whoopie Pies in the refrigerator until you are ready to serve them. This allows the frosting to firm up slightly and enables all the incredible flavors to meld beautifully. If desired, a light dusting of powdered sugar right before serving adds an elegant finishing touch. Store any leftover pumpkin whoopie pies in an airtight container in the refrigerator for up to 3 days. For longer-term storage, they freeze exceptionally well for up to 2 months. Simply thaw them gently in the refrigerator before enjoying.