Name: Healthy Pumpkin Whoopie Pies (Gluten-Free)
Prep time: 15 min
Cook time: 15 min
Total time: 30 min
Ingredients: 2 cups Almond Flour (Finely ground); 1.5 teaspoons Pumpkin Spice; 0.5 teaspoon Baking Soda; 0.25 teaspoon Salt; 1 cup Pumpkin Puree (Not pumpkin pie filling); 2 large Eggs (Room temperature); 0.33 cup Maple Syrup; 0.25 cup Coconut Oil (Melted and slightly cooled); 4 ounces Cream Cheese (Softened); 2 tablespoons Maple Syrup (For filling); 1 teaspoon Vanilla Extract (For filling)

Jump to Recipe

Creamy, spiced, and perfectly soft — these Healthy Pumpkin Whoopie Pies (Gluten-Free) are fall comfort in every bite. Imagine a tender pumpkin cake sandwich hugging a lightly sweet cream cheese filling; they’re cozy, lightly sweet, and surprisingly simple to make. Fun fact: whoopie pies are said to have originated as a treat Amish children would shout “Whoopie!” about when they found one in their lunchbox — and that same excitement hits every time you bite into these.

This recipe stands out because it’s gluten-free without sacrificing texture or flavor, and it comes together fast enough for weeknight baking. It’s family-friendly, crowd-pleasing, and pairs perfectly with a hot cup of tea. If you loved our take on pumpkin bars, you’ll find these just as comforting and a bit more portable — and for another spin on whoopie pies, check out this decadent option here: German Chocolate Whoopie Pies. Give these a try and get ready for compliments from kids and grown-ups alike!

What is Healthy Pumpkin Whoopie Pies (Gluten-Free)?

What’s in a name? Healthy Pumpkin Whoopie Pies (Gluten-Free) sounds like a dessert that went to the gym — but really it’s just a clever, wholesome twist on a classic. Whoopie pies are essentially two soft cookies sandwiched around a creamy filling; swap in pumpkin and almond flour, and you’ve got a seasonal, nutrient-forward version that’s still indulgent. Why “healthy”? Because these use almond flour and natural sweetener and skip the refined white flour. And yes, as the old saying goes, “the way to a man’s heart is through his stomach.” Who wouldn’t melt over a soft pumpkin sandwich cookie? Try them yourself and see whether they inspire a “whoopie” at your table.

Why You’ll Love This

Main highlight: The soft, spiced pumpkin cookie meets a tangy, silky cream cheese filling — warm spices and creamy sweetness in every bite.
Cost-saving: Making them at home is cheaper than buying specialty gluten-free desserts, and you control sweetness and quality of ingredients.
Flavorful toppings and add-ins: Toasted pecans, a dusting of cinnamon, or a drizzle of extra maple syrup take these from simple to show-stopping.

Compared to our pumpkin pie bars, these are smaller, portable, and perfect for lunchboxes or gatherings — a little more playful and easier to share. Ready to bake? You’ll love how quick they come together and how naturally delicious they are. Try them at home and watch how fast they disappear!

How to Make: Quick Overview

This recipe is delightfully straightforward: mix dry ingredients, blend wet ingredients, combine, drop rounds, bake, and sandwich with a silky cream cheese filling. The texture is soft and cakey with a light, creamy center. Standout element: the pumpkin adds moisture and warmth while almond flour keeps them tender and gluten-free.

Prep time: about 15 minutes
Baking time: 12 to 15 minutes
Total time: about 35 minutes
Yields: approximately 12 whoopie pies (depending on size)

Ingredients

2 cups almond flour, finely ground
1/3 cup maple syrup
1 cup pumpkin puree (not pumpkin pie filling)
2 large eggs, room temperature
1 1/2 teaspoons pumpkin spice
1/2 teaspoon baking soda
1/4 teaspoon salt
1/4 cup coconut oil, melted and slightly cooled
4 ounces cream cheese, softened (for filling)
2 tablespoons maple syrup (for filling)
1 teaspoon vanilla extract (for filling)

Directions

Preheat your oven to 350°F (175°C) and line a baking sheet with parchment paper for easy removal and cleanup.
In a medium bowl, whisk together the almond flour, baking soda, salt, and pumpkin spice until evenly combined. This ensures even spice distribution and lifts the crumb.
In a separate large bowl, mix the pumpkin puree, eggs, melted coconut oil, and 1/3 cup maple syrup until the mixture is smooth and well blended.
Gradually add the dry ingredients to the wet ingredients, stirring gently until just combined — be careful not to overmix, or the texture can become dense.
Using a tablespoon or cookie scoop, drop dollops of batter onto the prepared baking sheet, spacing them about 2 inches apart to allow spreading.
Bake for 12 to 15 minutes or until the tops are set and a toothpick inserted in the center comes out clean. Start checking at 12 minutes to avoid overbaking.
Remove from the oven and transfer the cookies to a wire rack to cool completely before filling so the cream cheese won’t melt.
For the filling, beat the softened cream cheese with 2 tablespoons maple syrup and 1 teaspoon vanilla extract until smooth and creamy. Taste and adjust sweetness if desired.
Spread a generous tablespoon of cream cheese filling onto the flat side of one cookie, then sandwich it with another cookie. Press gently to spread the filling evenly.
Repeat with remaining cookies and filling. Serve immediately or refrigerate to allow the filling to firm up slightly before enjoying your healthy pumpkin whoopie pies!

Healthy Pumpkin Whoopie Pies (Gluten-Free)

What to Serve With

Hot beverages: spiced latte, chai tea, or a bold black coffee to balance sweetness.
A scoop of dairy-free vanilla ice cream for an indulgent dessert pairing.
Fresh fruit: sliced apples or pear salad with a lemon-honey dressing to add crisp freshness.
A light green salad with toasted seeds for a contrasting savory bite if serving as part of a party spread.

Top Tips for Perfecting

Ingredient substitutions: Use sunflower seed flour if allergic to nuts, and swap coconut oil for melted butter for a richer flavor (not GF change).
Timing: Don’t overbake — remove when tops are set. They continue to firm as they cool.
Flavor boost: Fold in a pinch of ground ginger or a splash of molasses for deeper warmth.
Filling texture: Make sure cream cheese is fully softened for a smooth filling; chill briefly if you prefer a firmer sandwich.
Common mistakes: Overmixing almond flour can make cookies dense. Measure almond flour by spooning into the cup and leveling — avoid packing.

For another gluten-free pumpkin treat idea, try these pumpkin pie bars: Healthy Pumpkin Pie Bars.

Storing and Reheating Tips

Refrigeration: Store assembled whoopie pies in an airtight container in the refrigerator for up to 4 days. The cream cheese filling requires refrigeration.
Freezing: Freeze unfilled cookies in a single layer on a baking sheet; once solid, transfer to a freezer bag for up to 2 months. Thaw, then fill for freshest texture.
Shelf life: Assembled and refrigerated, they stay best for 3 to 4 days.
Reheating: Let refrigerated whoopie pies sit at room temperature for 10–15 minutes before serving for a softer bite. Avoid microwaving assembled sandwiches, which can make the filling too soft.

FAQs

Can I make these dairy-free?
Yes. Use dairy-free cream cheese (like almond or soy-based) for the filling and check that your coconut oil and other ingredients meet your dietary needs.

Can I use a different flour instead of almond flour?
Almond flour gives a moist, tender texture. You can try a 1:1 gluten-free flour blend, but expect slightly different texture and possibly the need for an extra egg or binder.

Are these suitable for kids?
Absolutely — they’re mildly sweet and soft, making them perfect for lunchboxes or after-school snacks. Keep refrigerated if packed early.

Can I make the filling ahead of time?
Yes, make the filling up to 2 days ahead, store it covered in the fridge, and whip briefly before assembling to refresh texture.

How can I make them sweeter or less sweet?
Adjust the maple syrup in the batter up or down by a tablespoon or two and taste the filling before assembling to balance sweetness.

Conclusion

These Healthy Pumpkin Whoopie Pies (Gluten-Free) are proof you can have both comfort and wholesome ingredients on the same plate — tender pumpkin cookies with a silky cream cheese center that’s quick to make and hard to resist. They’re easy enough for a busy weeknight bake and special enough for sharing at gatherings. For more recipe inspiration and variations on gluten-free pumpkin whoopie pies, check out this helpful guide: Gluten-Free Pumpkin Whoopie Pies – Meaningful Eats. If you’re looking for another refined-sugar-free take, see this lovely version here: Pumpkin Whoopie Pies + Gluten-Free, Refined Sugar-Free ….

Give these a try, share with loved ones, and enjoy the little “whoopie” moments around your table.