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    Home » Seasonal » Thanksgiving » Keto Pumpkin Whoopie Pies with Cream Cheese Filling

    Keto Pumpkin Whoopie Pies with Cream Cheese Filling

    lainey in the kitchen
    Modified: Nov 4, 2025 · Published: Oct 1, 2020 by Lainey · This post may contain affiliate links · 2 Comments
    Jump to Recipe Pin Recipe

    Soft and lightly spiced Keto Pumpkin Whoopie Pies with Cream Cheese Filling sandwiched together with a decadent, yet easy to make, pecan frosting! And it's keto-friendly!

    For more pumpkin recipes, try this Pumpkin Oreo Cheesecake and this No Yeast Pumpkin Cinnamon Rolls. Or Homemade Vegan Pumpkin Brownie.

    3 pumpkin whoopie pies in a white dish surrounded by a bowl of cream cheese and pecans

    A whoopie pie is either a cookie, pie,  or cake dessert — usually 2 round mound-shaped pieces of a flavored cake with a sweet and creamy filling sandwiched in between.

    Jump to:
    • Ingredients
    • Instructions
    • Substitutions
    • Variations
    • Storage
    • Top Tips
    • FAQ
    • Keto Pumpkin Whoopie Pies with Cream Cheese Filling

    Ingredients

    Listed below are all the ingredients you will need:

    Whoopie Pies:

    • butter
    • Swerve Granular Sugar
    • eggs
    • vanilla extract
    • pumpkin puree
    • baking powder
    • baking soda
    • cinnamon
    • pumpkin spice
    • salt
    • almond flour
    Ingredients for pumpkin whoopie pies

    Pecan Filling:

    • butter
    • cream cheese
    • pecans
    • Swerve confectionary sugar
    • vanilla extract
    ingredients for pecan cream cheese frosting

    Instructions

    Whoopie Pies:

    Preheat oven to 350 degrees F and line pan with parchment paper or baking mat.

    mixed melted butter and sugar

    In a large bowl, add the melted butter, sugar, and mix until light and fluffy. 

    added the eggs and vanilla extract to butter liquid mixture

    Next, add in the eggs, vanilla extract and whisk until well combined.

    rest of the ingredients added to the same bowl

    In the same bowl, mix together the rest of your ingredients.

    mixed bowl for keto pumpkin pies

    Combine them well.

    pumpkin cookie dough flatten on baking sheet

    Using a small cookie scoop, scoop the cookie dough onto a baking sheet and flatten leaving at least 2 inches between each cookie.

    baked keto pumpkin whoopie pie

    Place into oven at 350 fahrenheit

    Pecan Filling:

    mixed butter and cream cheese

    To make the pecan filling, in a large bowl, beat butter and cream cheese until light and fluffy. Then add powdered sugar, vanilla extract and mix until it is smooth.

    crushed pecans added to mixture

    Finally, add the crushed pecans and mix until just combined.

    Assemble:

    To assemble, using a cookie scooper, place a dollop of the filling in the center of the flat side of one a cookie.

    Place a matching piece of the cake against the filling and push to spread the filling evenly between the two halves. Repeat until all of the pies have been filled.

    whoopie pies being filled with pecan frosting on a cookie sheet

    Enjoy within the next same day, or refrigerate any leftover whoopie pies.

    Substitutions

    • Try different spices like ginger or cloves for unique flavors.
    • Swap Swerve granular sugar with your preferred sweetener.
    • Use a hand mixer instead of an electric mixer for convenience.
    • Bake the whoopie pies in batches of 2-3 to save time.
    • Pipe the dough onto the baking sheet for uniform shapes.
    • Substitute butter with coconut oil and cream cheese with a dairy-free alternative for a dairy-free option.

    Variations

    • Feel free to get creative with your whoopie pie presentation by adding decorative touches such as sprinkles or chopped nuts on top.

    Storage

    Store leftover whoopie pies in an airtight container in the refrigerator. They'll stay fresh for 3-4 days. For longer storage, wrap them individually in plastic wrap and freeze them. Thaw in the refrigerator before enjoying again.

    3 whoopie pies in a white dish surrounded by cream cheese frosting and sprinkles of pecans

    Top Tips

    • For this recipe, use pure canned pumpkin and not pumpkin pie filling.
    • Baking time. I like to slightly underbake the cookies to keep them soft, moist, and a little bit dense. If they are overbaked they lose their texture.
    • Cream Cheese.  It's important to soften the cream cheese before making the cream cheese frosting. I found that it won't combine as smoothly and you'll get cream cheese chunks in the frosting. I learned this the hard way.
    • Make-ahead: Cakes and frosting can be made a day ahead and stored separately in an airtight container. Allow the frosting to warm slightly at room temperature before filling.

    FAQ

    Is canned pumpkin keto friendly?

    Yes, canned pumpkin is generally keto-friendly because it's low carb and high in fiber, but be sure to check the label for added sugars.

    Why do my whoopie pies come out flat?

    If your whoopie pies come out flat, it could be due to overmixing the batter, not using enough leavening agents, or the oven temperature being too high.

    Why do my whoopie pies crack?

    Whoopie pies may crack if the batter is too dry or if they're overbaked, causing them to lose moisture and become brittle. Try adjusting the moisture level in the batter and monitoring the baking time closely.

    delicious whoopie pies on a table with cream cheese filling
    5 from 3 votes
    Print Pin Recipe

    Keto Pumpkin Whoopie Pies with Cream Cheese Filling

    Soft and lightly spiced Keto Pumpkin Whoopie Pie sandwiched together with a decadent, yet easy to make, pecan frosting! And it's keto-friendly
    Prep Time10 minutes mins
    Bake Time15 minutes mins
    Total Time25 minutes mins
    Course: Cookies, Desserts
    Cuisine: American
    Keyword: keto whoopie pies
    Servings: 6 large whoopie pies
    Calories: 208kcal
    Author: Lainey
    Prevent your screen from going dark

    Ingredients

    Whoopie Pies:

    • ¼ cup butter melted
    • ¾ cup Swerve Granular Sugar
    • 2 eggs
    • 1 teaspoon vanilla extract
    • ½ cup pumpkin puree
    • ½ teaspoon baking powder
    • ½ teaspoon baking soda
    • 1 teaspoon of cinnamon
    • 1 teaspoon of pumpkin pie spice
    • ⅛ teaspoon of salt
    • 1 cup almond flour

    Filling:

    • 6 tablespoons of soft butter
    • 4 ounces cream cheese
    • 3 tablespoons crushed pecans
    • 1 cup of Swerve confectionary sugar
    • 1 tablespoon of vanilla extract

    Instructions

    Whoopie Pies:

    • Preheat oven to 350 degrees F and line pan with parchment paper or baking mat.
    • In a large bowl, add the melted butter, sugar, and mix until light and fluffy.  Next, add in the eggs, vanilla extract and mix until well combined.
    • In the same bowl, mix together pumpkin puree, baking powder, baking soda, cinnamon, pumpkin pie spice, salt, and  almond flour.
    • Using a small cookie scoop, scoop the the cookie dough onto cookie sheet and flatten leaving at least 2 inches between each cookie.
    • Bake for  10-12 minutes for small cookies and 12-15 minutes for medium size cookies . Cookie edges will be brown when cooked.
    • Allow the cookies to cool completely before adding the filling.

    Filling:

    • In a large bowl, beat butter and cream cheese until light and fluffy. Then add powdered sugar, vanilla extract and mix until it is smooth. Finally add the crushed pecans and mix until just combined.

    Assemble:

    • Using a cookie scooper, place a dollop of the filling in the center of the flat side of one a cookie. Place a matching piece of the cake against the filling and push to spread the filling evenly between the two halves. Repeat until all of the pies have been filled.
    Leave a Comment
    Calories: 208kcalCarbohydrates: 7gProtein: 8gFat: 18gSaturated Fat: 5gPolyunsaturated Fat: 1gMonounsaturated Fat: 2gTrans Fat: 0.01gCholesterol: 75mgSodium: 218mgPotassium: 102mgFiber: 3gSugar: 3gVitamin A: 3527IUVitamin C: 1mgCalcium: 102mgIron: 1mg
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    Comments

      5 from 3 votes (1 rating without comment)

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      Recipe Rating




    1. Claire M says

      April 17, 2024 at 11:57 am

      5 stars
      This looks delicious and pretty easy too. Yum!

      Reply
    2. Liz L says

      April 18, 2024 at 10:14 am

      5 stars
      I used regular sugar and it turned yummy. A bit on the sweet side though.

      Reply

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