Keto Pumpkin Whoopie Pies
Published September 25, 2022 • Updated March 1, 2026
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Soft, spiced pumpkin cookies sandwiched around a thick cream cheese filling. I tested this recipe more times than I can count, and at 1.4g net carbs per cookie, it never gets old.
I started making these every Fall around 2019, and they have become one of my favorite seasonal treats. The pumpkin cookie itself is soft and chewy with warm spice running through every bite, and the cream cheese filling adds just enough richness to hold the whole thing together. At only 1.4g net carbs per cookie, I can keep a batch around all week without worrying about it.
The secret to these keto pumpkin whoopie pies is the combination of almond flour and oat fiber. I tested batches with almond flour alone, and they were fine but a little dense. Adding oat fiber gives the cookies a lighter crumb and a subtle oat flavor without adding any net carbs. If you have tried my keto oatmeal cream pies, you already know how well oat fiber works in sandwich cookies.
I use baking soda instead of baking powder here on purpose. These cookies need to stay flat so they sandwich together without wobbling. Baking powder would puff them up too much. It is a small detail, but it makes a real difference when you are stacking filling between two rounds.
The cream cheese filling comes together fast. I whip the butter first until it is fluffy, then fold in the sweetener and cream cheese. If your filling is too stiff to spread, a teaspoon or two of heavy cream loosens it up perfectly. I pipe mine with a pastry bag for even distribution, but a butter knife works if you are not fussy about presentation.
If you love pumpkin season as much as I do, pair these with my keto pumpkin cheesecake for a full spread, or bake a batch of healthy pumpkin cookies for something simpler. Either way, Fall baking stays low carb without tasting like a compromise.
How to make pumpkin whoopie pies
- Make the pumpkin cookie batter. Whisk almond flour, oat fiber, pumpkin pie spice, baking soda, and salt in one bowl. In a separate bowl, beat eggs and sugar free brown sugar on medium-high for a full 3 minutes (this is non-negotiable for fluffy texture). Stir in pumpkin puree and melted butter, then fold in the dry ingredients.
- Bake the cookies. Pipe or scoop 1-tablespoon mounds onto a parchment-lined sheet and bake at 350 for 12 minutes. They will look soft when you pull them out. That is normal. They firm up as they cool.
- Make the cream cheese filling. Whip softened butter until fluffy, mix in sugar free powdered sweetener, then add cream cheese and beat for 2 minutes.
- Assemble the pumpkin whoopie pies. Spread or pipe about half a tablespoon of filling between two same-sized cookies.
Key ingredients and substitutions
- Almond flour – The base flour here. I prefer a finely ground brand because it gives a smoother cookie. If you are used to baking with almond flour from recipes like my keto chocolate chip cookies, the same bag works.
- Oat fiber – Made from finely ground oat husks. It is zero net carbs and gives these cookies a lighter texture with a hint of oat flavor. Substitution: use 3/4 cup almond flour and 1/4 cup lupin flour if you do not have oat fiber.
- Pumpkin pie spice – I use a full teaspoon for stronger flavor. No pumpkin pie spice? Mix 1/2 teaspoon cinnamon, 1/4 teaspoon ground ginger, 1/8 teaspoon ground nutmeg, and 1/8 teaspoon ground cloves.
- Baking soda – I chose baking soda over baking powder specifically to keep these cookies flatter. For a sandwich cookie, you want less rise so they stack evenly.
- Brown sugar free sweetener – I have tested Lakanto, Swerve, and Truvia brown sugar alternatives. All three measure cup for cup with regular brown sugar and work well here.
- Pumpkin puree – Use canned 100% pumpkin puree, not pumpkin pie filling (which has added sugars). Homemade puree works too, but canned is easier and more consistent.
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Keto Pumpkin Cookies Ingredients
1 ¼ cup almond flour -
2 tablespoons oat fiber
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1 teaspoon baking soda
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1 teaspoon pumpkin pie spice
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¾ teaspoon salt
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2 eggs
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½ cup sugar-free brown sugar
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1 cup 100% pumpkin puree
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6 tablespoon unsalted butter, melted
Sugar Free Cream Cheese Filling Ingredients
-
4 tablespoons unsalted butter, softened
-
½ cup sugar-free powdered sugar
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4 oz cream cheese, softened
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1-3 teaspoons heavy cream, optional
Chocolate Drizzle (optional) Ingredients
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3 tablespoons sugar-free chocolate chips
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1 teaspoon coconut oil
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1/4 scoop Cacao Bliss
Step by Step Instructions
Step by Step Instructions
Combine dry ingredients
In a small bowl, combine almond flour, oat fiber, baking soda, pumpkin pie spice and salt. Set aside.
- Almond flour
- Oat fiber
- Baking soda
- Pumpkin pie spice
- Salt
Combine wet ingredients
In a large bowl, whip the eggs and sugar free brown sweetener (on medium-high speed of an electric or stand mixer) until fluffy (about 3 minutes). Reduce speed to low and stir in pumpkin and melted butter until just combined.
- Eggs
- Sugar-free brown sugar
- Pumpkin puree
- Butter (melted)
Combine dry and wet ingredients
Slowly stir in almond flour mixture and mix until just combined.
- Dry ingredients
Pipe or scoop
Add cookie dough to a pastry bag and pipe 1 tablespoon mounds of batter onto a parchment lined baking sheet, spacing them about 1 “ apart. Or scoop about a tablespoon using a spoon.
Time to bake
Bake at 350 degrees for 12 minutes. Remove from oven and let cool on the baking tray for 2-3 minutes until transferring to a wire rack to cool and set completely. Cookies will be soft when they first come out of the oven but will firm up as they cool.
Cream cheese filling
To make the filling, add butter to a medium bowl and whip with an electric mixer until fluffy. Add powdered sweetener and mix until combined, followed by the cream cheese. Continue mixing for 2 minutes. If your filling is too firm and not easily spreadable, add 1-3 teaspoons heavy cream to thin out the frosting.
- Butter (softened)
- Sugar-free powdered sweetener
- Cream cheese (softened)
- Heavy cream (if needed)
Assemble the whoopie pies
To assemble the whoopies, spread about ½ tablespoon filling in between two cookies that are about the same size. You can also use a piping bag to pipe a small amount of the filling.
- Two pumpkin cookies (about the same size)
- Cream cheese filling
Optional chocolate drizzle
Add chocolate chips and coconut oil to a small bowl. Microwave at 30 second intervals until melted, stirring in between. Stir in Cacao Bliss (if using). Drizzle on top of each pumpkin whoopie pie.
- Chocolate chips (sugar free)
- Coconut oil
- Cacao Bliss
Nutrition disclaimer
The nutrition information provided is an estimate and is for informational purposes only. I am a Doctor of Pharmacy (Pharm.D.); however, this content is not intended to be a substitute for professional medical advice, diagnosis, or treatment. Always consult your physician or other qualified health provider before making any lifestyle changes or beginning a new nutrition program.
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Get My Macros + Recipes →Frequently Asked Questions
Can I freeze keto pumpkin whoopie pies?
I freeze these all the time. Lay assembled cookies on a sheet pan in a single layer, freeze for an hour until firm, then move them to a freezer bag. They last about 2 months. I pull them out 15-20 minutes before serving and they taste just as good as fresh. You can also freeze the cookies alone (without filling) for up to 3 months and fill them the day you serve.
Can I make these ahead of time?
I do this for every holiday. Bake the cookies and make the cream cheese filling up to 3 days ahead. I store them in separate containers in the fridge, then assemble right before serving. The cookies hold their texture well in the fridge, and the filling actually pipes better when it is chilled.
Can I use coconut flour instead of almond flour?
I have tested coconut flour in these, and it works but you need way less. Coconut flour absorbs much more liquid, so I use about 1/3 cup coconut flour to replace 1 1/4 cups almond flour, and I add an extra egg to keep the batter from getting too dry. The texture comes out slightly denser, but still good.
Is pumpkin keto?
I use pumpkin in my baking all Fall long. It has more carbs than some squash, but one cup of puree is about 12g net carbs, and that gets split across 24 cookies in this recipe. Per serving, it barely registers. I keep a few cans in my pantry from September through December.
Is oat fiber keto friendly?
I use oat fiber in a lot of my baking. It is made from ground oat husks, and since it is all insoluble fiber, it is zero net carbs. It adds bulk and a subtle oat flavor to cookies and breads without spiking your carbs. I buy mine online because most grocery stores do not stock it.
Can I make these dairy free?
I have made the cookies with melted coconut oil instead of butter and they turn out well. For the filling, I swap the cream cheese for a plant-based cream cheese (Kite Hill works best in my experience) and use coconut oil in place of the butter. The filling is a little softer, so I chill it for 30 minutes before piping.
Can I add maple flavoring to the cream cheese filling?
One of my readers, Dan, added about 1/4 teaspoon maple extract to the filling and said it was a completely different cookie in the best way. I tried it after reading his comment and he was right. It adds a warm, almost caramel note that pairs perfectly with the pumpkin spice. If you like maple, check out my keto maple bacon cookies too.
How many cookies does this recipe make?
I get about 48 cookies from one batch, which means 24 assembled sandwich cookies once you pair them up. I use a tablespoon measure for each mound of batter to keep them consistent in size. A piping bag helps here because you get more uniform rounds than scooping by hand.
Mine took closer to 14 minutes, but worth it.
Mine were done at 14 before. Sounds like your oven runs a little hot, Yuki, once you know that it's easy to adjust.
1.4g net carbs per cookie. Checked three times.
One cup of pumpkin across 24 cookies, the math just barely holds. Ran it myself a dozen times before I stopped questioning it.
Several batches in, and the filling is still the thing I keep adjusting. A tablespoon of sour cream in the cream cheese loosens it enough to pipe cleanly and cuts the sweetness so the pumpkin pie spice actually comes through. Without it, mine were almost too rich to eat more than one, which felt like a waste at 1.4g net carbs each. I also started refrigerating the assembled pies for about an hour before serving, and the texture goes more brownie-dense than cakey. That version I like more than fresh. Don't push past 12 minutes: at 13 or 14 the edges firm up and you lose the soft, pillowy texture that makes the sandwich work.
The sour cream in the filling is smart. Acid cuts through the fat and that's why the spice actually registers. And the refrigerated version, I've made them a day ahead and preferred them cold too, I just never say that out loud because everyone wants to eat them immediately.
Mine go in the fridge overnight now and I've stopped serving them fresh.
work potluck hero. didn't even get one myself.
Save one before you even walk in the door next time.
Batch made these on a Sunday, actual cool weather for once, and I'm glad I doubled the recipe. The cream cheese filling firms up overnight and the pumpkin flavor deepens on day two. Didn't see that coming. I store the assembled ones in a single layer and they hold cold, which matters when I'm grabbing one before work. 1.4g net carbs each, so I pack two and don't think about it again until dinner. The oat fiber is doing something for texture that keeps them from going soggy with the filling inside, even after four days. Making another batch this weekend.
Day two is the better batch. The spice settles and the cream cheese has set into the cookie instead of just sitting between them. I stopped eating these same-day.
Browned the butter before adding it in and the cookies came out with this deeper, almost caramel-y edge that I was not expecting. If you're already melting it anyway, the extra 3 minutes is worth it.
The caramel-y thing is the milk solids browning. Brown butter and pumpkin spice together, I'm annoyed I haven't tried this yet.
Made a double batch on Sunday and froze the cookies without the filling, and this might be the smartest thing I've done in months. Pulled out four this morning, piped the cream cheese straight from the fridge while they thawed for maybe ten minutes, and now I have pumpkin whoopie pies ready before I've had coffee. Filling holds up perfectly, cookies don't get soggy or weird, and at 1.4g net carbs I'm not even thinking twice about eating dessert at 7am. Double batch only from here on out.
Piping the filling cold actually holds the swirl better. I've always frozen them assembled but your method gets you pumpkin whoopie pies at 7am, so I'm reconsidering.
My daughter grabbed one from the fridge this morning and asked if I ordered them somewhere. She's eight and has never asked for a second keto anything. Twenty minutes later she quietly took another one. The cream cheese filling got her, I'm pretty sure.
The quiet second one is the real review. Eight-year-olds don't fake it.
Brought these to my sister's baby shower and someone actually flipped one over looking for a bakery label. She could not believe they were homemade. That cream cheese filling is SO good.
Baby shower is a tough room. The filling is what gets people every time.
I've worked through probably four other keto pumpkin cookie recipes and every single one came out dense and dry, the kind you eat because it's technically dessert, not because you actually want it. These are actually soft in the middle. I think the oat fiber is doing something I haven't seen in any other version, because nothing else I've tried has had that texture. The cream cheese filling is the right thickness too, not that thin smear you get when the ratio is off. This is the one I'm sticking with.
Oat fiber is carrying this one. Nothing else behaves like it in pumpkin baking.
This is my fourth time making these and I think I finally nailed the piping situation, because I was just dropping them with a spoon before and they kept spreading too flat, but once I actually used a pastry bag they came out looking like the photo and the filling to cookie ratio was so much better. I also added a little extra pumpkin pie spice this batch, maybe half a teaspoon more than the recipe calls for, and the spice came through so much more in the cookie. The cream cheese filling is already thick and tangy on its own so a little more warmth in the cookie actually balanced things out in a way I liked a lot. Started a batch last week because I convinced myself pumpkin is a year-round thing and I don't regret it, the house smelled like a fall bakery for two hours, which felt very strange for April and also completely worth it. Double batch next time so I can actually freeze some before they disappear.
The piping bag matters more than people expect, the batter stays where you put it instead of spreading. I go 1 1/2 teaspoons on the spice sometimes too, depends on the puree brand (they vary more than you'd think). Freeze half before they're gone.
Whoopie pies were the one thing I thought I was just done with on keto. That cream cheese filling comes together so thick, and at 1.4g net carbs I had two without a second thought.
Two without counting is the whole point. If you want to change up the filling next time, try 1/4 tsp maple extract in it. One of my readers tipped me off and I tested it after. Different cookie.
Brought these to my sister's Easter dinner and two people who'd skip anything labeled keto were scraping the last of the cream cheese filling off the wrappers with their fingers. Not exactly a subtle reaction.
Scrapers at Easter. Two people who'd normally pass on anything keto cleaning the wrappers is the review I care about.
Been through a handful of keto whoopie pie recipes and most of them get the filling wrong, either too soft or just cream cheese with sweetener dumped in. This one actually holds, and the pumpkin spice in the cookie is present without being aggressive.
The filling took a few tries to get right. Too much cream cheese and it goes soft, too little and it's just sweet. And yeah, one teaspoon of pumpkin spice was on purpose. Any more and it takes over.
Added a splash of vanilla to the cream cheese filling and I think it actually needed it. The tang softened a bit and the whole thing tasted more like the whoopie pies I used to get at fall bakeries.
Yeah, vanilla balances the cream cheese tang without covering it. The classic whoopie pie filling is much sweeter so that tracks. I'd try 1/4 tsp next batch.