Pumpkin Bread Keto Whoopie Pies are here just in time for the fall! These low-carb whoopie pies feature delicious pumpkin bread layers stuffed with a sweet cream cheese frosting inside. These whoopie pies are also grain-free, and gluten-free!

We are talking pumpkin overload! They are made with pumpkin puree and taste and smell like pumpkin spice!
They are delicate and fall apart in your mouth. And they are keto-friendly!
For more pumpkin keto recipes, be sure to try our Keto Pumpkin Cream Cheese Muffins and Keto Pumpkin Cake Pops!
Why You Will Love these Pumpkin Bread Keto Whoopie Pies!
- Easy: It takes less than 30 minutes to whip up a batch of these handheld pumpkin treats!
- Low carb: Each whoopie pie contains only 3g of net carbs.
- Perfect for a crowd: This recipe makes 20 whoopie pies, so it's a great recipe if you are entertaining or need a dessert to bring to a party.
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Ingredients

First things things first, gather all of your ingredients and measure them out.
You will probably have most of the ingredients on hand in your pantry or fridge.
Here is a quick list of what you need:
Pantry Items
- Almond flour: Almond flour is a great gluten-free and keto-friendly alternative to all-purpose flour.
- Baking powder & baking soda: To help the pumpkin bread cookies rise when they bake.
- Ground cinnamon, pumpkin pie spice and salt: The perfect spices for that classic pumpkin flavor.
- Xanthan gum: Helps to bind the ingredients together.
- Vanilla extract: Use 100% pure for the best flavor and sweetness.
- Granular erythritol: Our favorite is Swerve. It has the best taste without any aftertaste.
- Confectioner erythritol: If you don't have this on hand, you can add granular erythritol to a food processor and process until if becomes a powder.
- Pumpkin puree: This should be pure pumpkin puree not pumpkin pie filling.
Fridge Items
- Butter: Use unsalted softened butter so that it combines easily with the other ingredients.
- Cream cheese: Again, this should be softened and use full-fat.
- Eggs: Use organic and pastured eggs if possible.

How to Make Pumpkin Bread Keto Whoopie Pies
These are pretty simple to make. You just have to bake the pumpkin bread cookies (your entire house will smell incredible as these are baking)!
Then whip up some keto cream cheese frosting, fill the cookies with the frosting, and try not to eat the entire batch at once.
It's tough, we know!
The full instructions are detailed in the recipe card at the end of this post.
But we wanted to give you step-by-step instructions, so you know exactly how to make these low-carb whoopie pies.
Step #1. Make the Pumpkin Bread Batter
We are going to start with the pumpkin bread cookies first.
In a large bowl, mix together the almond flour, baking powder, baking soda, cinnamon, pumpkin pie spice, xanthan gum, and salt.
In another large bowl, beat the butter with an electric mixer until it is fluffy, then add the erythritol and eggs.
Beat for 1 minute, then add in the pumpkin puree and vanilla and beat again for another minute.
Add your dry ingredients into the wet ingredients and mix until combined.
It should be a nice, thick batter (like the picture below).

Step #2. Bake the Pumpkin Bread Layers
Take roughly 1 tablespoon of batter and spoon it onto parchment paper lined baking sheets. Space the spooned batter 2 inches apart (like the picture below).
Wet your finger with water and smooth out each until it is a flat and 2-inch diameter circle. Bake at 350°F for 12 minutes or until the edges begin to brown.
The recipe makes 20 whoopie pies, which means you need 40 individual pumpkin bread cookies. We used two half-size baking sheets (16x12 inches), which made 12 cookies each and then baked them in two separate batches.
If you don't have multiple baking sheets, just make them in batches like us. The cookies only take 12 minutes to bake, so it won't add much extra time.

Step #3. Make the Filling
While the cookies are baking, make your filling.
All you need to do is add the ingredients to a mixing bowl and use an electric mixer to combine.
Using an electric hand mixer will get the filling really light and well-whipped.

Step #4. Assemble the Whoopie Pies
Now you are ready to frost the cookies. Before you start, make sure the pumpkin bread cookies are cooled complately.
Place about 2 tablespoons of filling on the bottom pumpkin bread cookie layer.
If your filling is too firm, microwave it for 10 seconds so that it is easier to spread onto your cookies.
Add another pumpkin cookie on top and gently press down so that the frosting spreads almost to the edge of the cookie layers.
Try to line up the bottom and top cookie layers so that the whole pumpkin whoopie pie looks neat and even.

Recipe Notes and Tips
- Work in batches if necessary. This recipe makes 20 whoopie pies, which means you need 40 individual pumpkin bread cookies. Work in batches if you don't have multiple baking sheets. The cookies only take 12 minutes to bake so it doesn't add much extra time.
- Baker's Full Sheet (26x18 inches) will fit 20 cookies.
- Baker's Half Sheet (16x12 inches) will fit 12 cookies.
- Use a cookie scoop. To keep all the pumpkin bread cookies the same size, use a cookie scoop (or small ice cream scoop) to measure out the batter. It's important to keep them the same size so they all cook in the same time. You don't want any to burn while others are still gooey.
- Let the pumpkin break cookies cool. Make sure the cookies are cooled off completely before adding the frosting. If you add it too soon while they are still warm, the frosting will melt.
- Use a piping bag. If you want the whoopie pies to have a pretty look to them, use a piping bag. Don't have a piping bag? Make your own by putting the frosting in a zippered plastic bag and cut a hole in the corner. If your frosting is too firm, microwave it for 10 seconds so that it is easier to spread onto your cookies.
Frequently Asked Questions
There are about 3g net carbs in each whoopie pie. That's it! So you really could eat a few of these at a sitting without hurting your macros.
Store any leftover whoopie pies in a sealed container at room temperature for one day and then store in the refrigerator for up to 7 days after that.
Whoopie pies are extremely versatile. Make sure to try our Zucchini Bread Whoopie Pies and our Red Velvet Whoopie Pies. Both versions are keto, low-carb, grain-free, and gluten-free!

More Keto Dessert Recipes
If you’d like more delicious desserts that are perfectly keto, then check out these favorites:
- Keto Pumpkin Cake Pops
- Keto Chocolate Loaf
- Keto Thin Mints
- Samoa Keto Doughnuts with Caramel and Chocolate
- Keto Coffee Cake
- Keto Pumpkin Pie
We Can't Wait To See You Try It!
We love seeing our recipes come to life!! We can’t wait to see how you make these easy keto whoopie pies and loving seeing each person's unique spin on it! Tag us on Instagram @cleanketolifestyle or use the hashtag #CKLrecipe!

Keto Pumpkin Bread Whoopie Pies
Ingredients
For the Pumpkin Bread Cookies
- 2 cups almond flour
- 1 teaspoon baking powder
- 1 teaspoon baking soda
- 1 1/2 teaspoons cinnamon
- 1 teaspoon pumpkin pie spice
- 1 teaspoon xanthan gum
- 1/2 teaspoon salt
- 1/2 cup softened butter
- 1 cup granular erythritol
- 2 eggs
- 1 cup pumpkin puree
- 1 teaspoon vanilla extract
For the Cream Cheese Frosting Layer
- 6 tablespoons softened butter
- 4 oz. softened cream cheese
- 1/2 teaspoon vanilla extract
- 1 cup confectioners erythritol
Instructions
For the Pumpkin Bread Cookies
- Heat your oven to 350°F and line a baking sheet(s) with parchment paper. (We used two half- sheets (16x12 inches) and baked the 40 cookies in two batches.)
- In a large bowl, mix together the flour, baking powder, baking soda, cinnamon, pumpkin pie spice, xanthan gum, and salt.
- In another large bowl, beat the butter with an electric mixer until it is fluffy, then add the granular erythritol and eggs.
- Beat for one minute, then add in the pumpkin puree and vanilla and beat again for another minute.
- Slowly, add your dry ingredients into the wet ingredients and beat until well combined.
- Take the batter 1 tablespoon at a time and spoon it onto the baking sheets.
- Wet your finger with water and smooth out the spoonfuls of batter until they are flat 2-inch diameter circles.
- Bake for 12 minutes or until the edges begin to brown.
- Let the pumpkin bread cookies cool completely before assembling the whoopie pies.
For the Cream Cheese Frosting Layer
- While the cookies are baking, make your filling.
- In a medium bowl, beat together the butter, cream cheese, and vanilla with an electric mixer for 1 minute.
- Slowly add in the confectioner erythritol, beating as you go. Beat for 2-3 more minutes.
Whoopie Pie Assembly
- Once the cookies have cooled, add your frosting to a piping bag or Ziploc bag with a hole cut in one corner.
- Pipe about 1 tablespoon of frosting onto the bottom cookie layer, if your frosting is too thick, you can microwave it for 10 seconds to soften it.
- Add the top cookie layer and gently press down so that the frosting spreads almost all the way to the outer edges.
Notes
- Work in batches if necessary. This recipe makes 20 whoopie pies, which means you need 40 individual pumpkin bread cookies. Work in batches if you don't have multiple baking sheets. The cookies only take 12 minutes to bake so it doesn't add much extra time.
- Baker's Full Sheet (26x18 inches) will fit 20 cookies.
- Baker's Half Sheet (16x12 inches) will fit 12 cookies.
- Use a cookie scoop. To keep all the pumpkin bread cookies the same size, use a cookie scoop (or small ice cream scoop) to measure out the batter. It's important to keep them the same size so they all cook in the same time. You don't want any to burn while others are still gooey.
- Let the pumpkin break cookies cool. Make sure the cookies are cooled off completely before adding the frosting. If you add it too soon while they are still warm, the frosting will melt.
- Use a piping bag. If you want the whoopie pies to have a pretty look to them, use a piping bag. Don't have a piping bag? Make your own by putting the frosting in a zippered plastic bag and cut a hole in the corner. If your frosting is too firm, microwave it for 10 seconds so that it is easier to spread onto your cookies.
Natalie
This is a wonderful recipe. Bake time was a little longer for me (maybe because of high altitude?). Cream filling was a little sweeter than our taste so I will be reducing the sweetener by 1/3-1/2. This is one of the best KETO bakery items I’ve tried that was DELICIOUS!
Clean Keto Lifestyle
Hi Natalie!! We are so glad you liked them! They really are delicious!