Keto Pumpkin Whoopie Pies (Makes Six)

Keto pumpkin whoopie pies with cream filling on a white platter, cinnamon sticks behind
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Introduction

A whoopie pie is a slightly odd thing to explain. It is not a pie and it is not really a cookie either — two soft, cake-like rounds with a thick layer of cream between them, closer to a small sandwiched cake than to anything you would put in a cookie jar.

That cake-like texture is the part that survives the keto version intact. Almond flour and pumpkin puree make a soft, moist cookie naturally, so there is no crispness to lose here in the first place.

The Dough Will Stick to You

It is sticky, and that is not a sign anything has gone wrong. Almond flour and pumpkin puree together make a batter closer to a thick paste than to a dough you could roll.

Wet your hands before you shape it and it stops clinging. Twelve balls, flattened slightly, well spaced on the sheet — and twelve cookies is six finished whoopie pies, which is worth holding onto when you are counting them out.

They come out of the oven soft and they stay soft. Do not wait for them to firm up or brown deeply; when the tops are set, they are done.

Let Them Cool. All the Way.

This is the step people lose patience with, and it is the one that decides the outcome.

The filling is cream cheese and butter beaten together with sweetener. Put that on a cookie that is even slightly warm and it does not spread — it slides, then it sinks into the cookie, and you end up with something you eat with a spoon. Chilling it afterwards firms the filling but does not lift it back out of the crumb.

So cool them completely, and use the refrigerator if you are in a hurry. Make the filling while you wait, which is the one place this recipe overlaps with itself.

The same logic applies afterwards: cream cheese and butter mean these keep in the refrigerator, not on the counter.

Keto Pumpkin Whoopie Pies

Prep Time
20 minutes
Cook Time
15 minutes
Total Time
35 minutes
Yield
6 servings
Course
Dessert
Cuisine
American

Ingredients

For the cookies

For the filling

Nutrition Facts

6 servings per recipe
Trans Fat 0g 0% 0g 0%
Total Sugars — —
Allulose 0g 0% 0g 0%

Where you see an em dash: one of the ingredients in this recipe does not publish a figure for that row, so we cannot add one up honestly. We would rather show you nothing there than a zero we cannot stand behind.

About these numbers: We are home cooks, not certified nutritionists. Nutrition is shared as a courtesy. We pick a representative product for each ingredient, and our recipe system works out the totals from the amounts in this recipe, so please treat them as a helpful estimate rather than a guarantee. The brands you buy, any swaps you make, and how generously you portion the recipe will all move these numbers.

Directions

  1. Prepare your oven and baking sheets.

    Make sure to start your oven early so it reaches the correct temperature. Preheat your oven to 350°F and line two baking sheets with parchment paper. A well-preheated oven is key to the perfect bake.

  2. Blend together the cookie ingredients.

    Mix the almond flour, pumpkin puree, pumpkin pie spice, swerve sweetener, vanilla, baking powder, and egg in a large bowl. Use your hand mixer or electric mixer to blend until light and fluffy to achieve a soft cookie texture.

  3. Form the mixture into 12 evenly-sized balls and flatten slightly.

    Wet your hands slightly with water, then scoop the dough into balls. Flatten them a bit on a baking sheet with parchment paper. Make sure they are well-spaced so they bake evenly and will not stick with each other.

  5. Bake for 12-15 minutes.

    They are done when the tops are set and lightly browned. These stay soft rather than crisping - a whoopie pie cookie is closer to a small cake than to a biscuit, so do not wait for a snap.

  6. Cool your cookies at room temperature.

    Allow your whoopie pie cookies to cool completely to make sure the cream cheese filling won't melt when spread. Place them in the fridge if you need to speed up the process.

  7. Blend together the filling ingredients until smooth and creamy.

    Combine softened cream cheese, butter, vanilla, and swerve confectioners until light and fluffy. Make sure it's smooth and creamy for that perfect whoopie pie filling.

  8. Assemble the keto whoopie pies.

    Flip a cookie upside down and place a 6th of the filling onto it. Add another cookie on top to form a whoopie pie. Repeat for the remaining whoopie pies.

  9. Continue assembling until all the keto whoopie pies are made.

    If you have a piping bag, you can use it to add the filling for a more polished look.

Notes

Shaping and Cooling

The dough is sticky, which is normal for almond flour and pumpkin puree together. Wet your hands before you scoop and it stops clinging to you.

Twelve balls, flattened slightly and well spaced. Twelve cookies makes six whoopie pies, so if you lose count, count in pairs.

Then let them cool completely before the filling goes anywhere near them. This is the step that decides whether you get a whoopie pie or a puddle — the filling is cream cheese and butter, and either one will slump off a cookie that is still warm. If you are impatient, the refrigerator will get you there faster.

Preparation

  • Sift the almond flour and baking powder, or at least whisk them. Almond flour lumps, and lumps do not break up once the pumpkin goes in.
  • Make the filling while the cookies bake and cool. It is the only way this recipe overlaps with itself.
  • If the butter for the filling is fridge-cold, grate it or cut it into small cubes — it softens much faster that way than sitting in a block.
  • Taste the filling before you use it and adjust the sweetener then, not after it is between two cookies.
  • A piping bag gives a neater edge than a spoon. A zip-top bag with a corner cut off does the same job.

Storage

Cream cheese and butter are what the filling is made of, so these live in the refrigerator rather than on the counter. Keep them in an airtight container, with parchment between the layers so they do not stick. We do not have a reliable number of days for them once they are assembled, or any freezing directions.

If you want one warm, a few seconds in the microwave is enough — any longer and the filling melts out of the middle.

Serving

They are rich — the filling is cream cheese and butter beaten with sweetener, and there is a thick layer of it in each one.

A dusting of powdered sweetener over the top is the easy way to make a plate of them look deliberate. Coffee or tea alongside, for the same reason it works with any cream-filled thing: it cuts the sweetness.

Frequently Asked Questions

What is a whoopie pie?

Two soft, cake-like rounds with a thick layer of sweet filling between them, eaten with your hands. Not a pie, and not really a cookie either — closer to a small sandwiched cake. Chocolate with vanilla filling is the version most people picture; this one is pumpkin.

Are whoopie pies and macarons the same thing?

No, and there are two different things they get confused with, which is worth untangling.

Macarons are the delicate sandwich ones — almond flour and egg-white meringue, smooth-shelled, with a thin filling. A whoopie pie is the opposite of delicate: two soft cake-like rounds with a thick layer of filling between them, closer to a cake you eat with your hands.

Macaroons, spelled with the second o, are different again — coconut, craggy, and not a sandwich at all.

Why are they called whoopie pies?

The story usually told is that Amish women packed them into their husbands’ and children’s lunchboxes, and that whoever opened the box shouted “Whoopie!” It is repeated everywhere and nobody has ever pinned it down, so treat it as the story rather than the history. The name stuck either way.

Are pumpkin whoopie pies sticky?

The finished rounds are soft and moist rather than sticky. What is soft at room temperature is the filling, so it will meet your fingers at the edges — these are eaten with a hand, not tidily.

The batter is another matter. Before it bakes it is closer to a thick paste than a dough, and it does stick to you. Wet your hands before you shape it.

How long do pumpkin whoopie pies keep?

We cannot give you an exact number of days. What sets the limit is the filling rather than the cookies, and it is cream cheese and butter, so these belong in the refrigerator.

They are at their best while the cookies are still soft.

Can I add more flavors to the keto pumpkin whoopie pies?

Spices are the easy one. Nutmeg or extra cinnamon go in with the dry ingredients and change nothing about how the batter behaves, so add them to taste.

Cocoa powder is a different proposition. It is a dry ingredient in its own right rather than a seasoning, so it changes the flour-to-liquid balance of a batter that already has to stay soft enough to sandwich. We do not have a cocoa amount for this batter, and guessing at one on something this soft is how you end up with rounds that crumble under the filling.

Can I use coconut flour instead of almond flour for this whoopie pie recipe?

Not as a straight swap, and we do not have coconut-flour amounts to give you instead.

Coconut flour absorbs several times the liquid almond flour does, so it is a reformulation rather than a substitution — you would be changing the flour quantity and the liquid together and judging the result yourself. On a soft cake-like round that has to hold a filling without crumbling, that is a lot to get right blind.

Can I freeze the whoopie pie filling separately?

We do not have freezing guidance for the filling on its own — no container, no thawing time and no step for bringing it back — so we cannot tell you how it comes through.

The filling is cream cheese and butter, which is why the assembled pies belong in the refrigerator rather than on the counter, and the recipe is written around a filling made fresh.

Wrap Up

Six is a slightly awkward number — enough to share, not enough to leave any behind.

They only take a third of a cup of pumpkin, so if the rest of the can is still in the fridge, our keto pumpkin recipes have plenty of places to put it.

Have you tried this recipe or any other recipe on the blog? Please rate it below and let us know what you think in the comments! We love hearing from you!

Oh, and remember to snap a pic of your take and share it on Instagram with the hashtag #buttertogetherkitchen.

Updated — September 18, 2026: The questions below now match the recipe, and the one about macarons explains what a whoopie pie is not — including the coconut macaroon it gets confused with.

Correction — September 18, 2026: One question still said these keep 2-3 days at room temperature after the card had been corrected. These keep in the refrigerator, not on the counter.