Keto Pumpkin Whoopie Pies with Cream Cheese Filling

These Keto Pumpkin Whoopie Pies, filled with a smooth cream cheese and crunchy pecan filling, are a quick and satisfying low-carb treat. Soft, pumpkin-spiced cookies sandwich a creamy filling for a dessert that’s both keto-friendly and irresistible.

Keto Pumpkin Whoopie Pies with cream cheese and pecan filling

Keto Pumpkin Whoopie Pies

I developed this Keto Pumpkin Whoopie Pies recipe while adapting classic flavors for a lower-carb lifestyle. Using almond flour for the cookie base and a cream cheese-pecan filling keeps the treats tender and flavorful without relying on wheat flour. They’re easy to make, freeze well, and are tasty enough to please non-keto friends and family.

steps for making the whoopie pies

Recipe for these pies

Ingredients for pies

  • 1 cup almond flour
  • ½ cup pumpkin puree
  • ¼ cup butter, melted
  • ¾ cup granular low-carb sweetener (e.g., Swerve)
  • 1 large egg
  • 1 teaspoon vanilla extract
  • 1 teaspoon ground cinnamon
  • 1 teaspoon pumpkin pie spice
  • ½ teaspoon baking powder
  • ½ teaspoon baking soda
  • ⅛ teaspoon salt

Ingredients for filling

  • 6 tablespoons butter, softened
  • 4 ounces cream cheese, softened
  • 1 cup confectioners-style low-carb sweetener (e.g., Swerve Confectioners)
  • 1 tablespoon vanilla extract
  • 3 tablespoons crushed pecans
steps for making the filling

How to make Keto Pumpkin Whoopie Pies

Time needed: About 45 minutes total (15 min prep, 15 min cook, 15 min cooling).

  1. Preheat. Preheat the oven to 350°F (175°C). Line baking sheets with parchment paper.
  2. Mix butter and sweetener. In a bowl, beat the melted butter with the granular sweetener until smooth.
  3. Add egg and vanilla. Stir in the egg and vanilla extract until well combined.
  4. Combine dry and wet. Add the almond flour, pumpkin puree, cinnamon, pumpkin pie spice, baking powder, baking soda, and salt. Mix for about 2 minutes until the batter is even and slightly thick.
  5. Scoop cookies. Using a small cookie scoop or teaspoon, portion the batter into even rounds on the prepared baking sheet. Leave at least 2 inches between each as they will spread slightly. Depending on size, you may need two sheets or multiple batches.
  6. Bake. Bake for 10–15 minutes, until the edges are lightly browned and the centers are set.
  7. Cool. Let the cookies cool on the pan until they are completely cool to the touch before assembling.
  8. Make the filling. Beat the softened butter and cream cheese together until smooth. Add the confectioners-style sweetener and vanilla and mix until creamy. Fold in the crushed pecans.
  9. Assemble. Spread a spoonful of filling on the flat side of one cookie and sandwich with another cookie. Repeat until all are assembled.
finished cookies with a bowl of pecans

Pumpkin Whoopie Pies: FAQs

Can you freeze Pumpkin Whoopie Pies?

Yes. Wrap each whoopie pie individually or layer them between parchment paper in an airtight container. They keep well in the freezer for up to two months. Thaw in the refrigerator or at room temperature before serving.

Should these be kept refrigerated?

Yes. Because the filling contains cream cheese and butter, store leftovers in a sealed container in the refrigerator for up to 5 days.

Where do whoopie pies come from?

The exact origin is debated, but whoopie pies are traditionally associated with New England and Pennsylvania Dutch baking traditions. They’re classic cake-like cookie sandwiches that became a regional favorite.

assembling the cookies

Tips: For consistent cookies, use a cookie scoop and weigh or measure your batter portions. If you prefer fewer, larger whoopie pies, bake larger rounds and increase baking time slightly. For a nut-free version, omit pecans from the filling and replace with toasted shredded coconut if desired.

finished pumpkin whoopie pie

Other recipes you may enjoy

  • Pumpkin Pecan Bread
  • Pumpkin Cupcakes with Pumpkin Spice Cream Cheese Frosting
  • Keto Pumpkin Pie Fat Bombs
  • Bacon Cheddar Ranch Chicken
  • Pumpkin Pie

Equipment

  • Measuring cups and spoons
  • Mixing bowls
  • Hand mixer or whisk
  • Rubber spatula or wooden spoon
  • Cookie scoop or teaspoon
  • Parchment paper and baking sheets

Notes

  • Yield varies by size: make about 12 small to medium whoopie pies, or 6 larger ones.
  • Adjust sweetness to taste depending on the low-carb sweetener you use.
  • Nutrition values are approximate and depend on specific ingredients and portion sizes.

Nutrition (approx. per serving)

Calories: 202 kcal, Carbohydrates: 26 g, Protein: 4 g, Fat: 20 g, Saturated Fat: 9 g, Fiber: 2 g, Sugar: 1 g.