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Keto Pumpkin Whoopie Pies

Keto pumpkin whoopie pies — soft, spiced pumpkin cookies sandwiched around a thick cream cheese filling, just 1.4g net carbs per cookie. I've tested this recipe more times than I can count, and it never gets old.
  • 1.4gnet carbs
  • 2.2gprotein
  • 37minutes
  • 24servings

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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.

closeup of melted chocolate on top of a pumpkin whoopie pie filled with cream cheese

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.

two whoopie pies stacked on each other with melted chocolate dripping down

What is a whoopie pie?

A traditional whoopie pie is two rounds of soft cake (usually chocolate) with vanilla buttercream and marshmallow fluff sandwiched between them. They are handheld, messy in the best way, and range from bite-sized to palm-sized depending on who is baking them.

I grew up seeing these at bakeries and church potlucks, and the classic versions are loaded with sugar. When I started adapting my favorite baked goods for low carb, this was high on my list. The pumpkin version swaps out the chocolate cake for spiced pumpkin cookies and uses a cream cheese filling instead of buttercream. If you like pumpkin in your Fall baking, try pairing these with my keto pumpkin chocolate chip cookies for a full cookie spread.

a bite out of a pumpkin whoopie pie stacked on a whole one with a white pumpkin in the background

Chocolate drizzle

I finish these with a quick chocolate glaze drizzled across the top of each cookie. To make it, I melt sugar free chocolate chips with a little coconut oil until smooth. The coconut oil thins the chocolate just enough for a clean drizzle and gives it a nice sheen once it sets.

For a deeper chocolate flavor with some warmth, I stir in a raw cacao powder blend with cinnamon and turmeric. I originally partnered with Earth Echo and used its Cacao Bliss for this recipe. It blends raw cacao with turmeric, black pepper, MCT powder, cinnamon, monk fruit, coconut nectar, lucuma, mesquite, and Himalayan salt. I like the warm, spiced chocolate flavor it adds to the glaze.

If you want to try Cacao Bliss, use code KETOFOCUS at checkout.

a blue bag of cacao bliss sits behind a plate of chocolate covered whoopie pies

How to store and freeze these cookies

I keep assembled cookies in an airtight container at room temperature for up to 5 days. The cream cheese filling stays stable, and the cookies actually get softer and chewier after day one. That makes them ideal for a holiday cookie exchange, Halloween party, or keto Halloween cookie spread.

For longer storage, I freeze them. Lay assembled cookies in a single layer on a sheet pan and freeze for about an hour until firm, then transfer to a freezer bag. They keep for up to 2 months this way. I pull them out 15-20 minutes before serving and they thaw perfectly. You can also freeze just the cookies without filling (up to 3 months) and fill them fresh when you are ready.

If you want to make these ahead, bake the cookies and make the filling up to 3 days in advance. Store them separately in the fridge, then assemble before serving. I do this for Thanksgiving every year so I am not scrambling with desserts. Pair them with my keto pumpkin cheesecake lasagna for a full sugar free dessert table.

How to make pumpkin whoopie pies

  1. 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.
  2. 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.
  3. 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.
  4. Assemble the pumpkin whoopie pies. Spread or pipe about half a tablespoon of filling between two same-sized cookies.

two pumpkin cookies filled with a cream cheese filling in front of a white pumpkin

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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The recipe

Keto Pumpkin Whoopie Pies

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Prep 25 min Cook 12 min Total 37 min Serves 24

Ingredients

Servings 24

Keto Pumpkin Cookies Ingredients

Sugar Free Cream Cheese Filling Ingredients

Chocolate Drizzle (optional) Ingredients

Step by Step Instructions

  1. Combine dry ingredients

    In a small bowl, combine almond flour, oat fiber, baking soda, pumpkin pie spice and salt. Set aside.

    For this step

    • Almond flour
    • Oat fiber
    • Baking soda
    • Pumpkin pie spice
    • Salt
    whisking dry ingredients in a glass bowl
  2. 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.

    For this step

    • Eggs
    • Sugar-free brown sugar
    • Pumpkin puree
    • Butter (melted)
    beating an egg mixture with an electric mixer
  3. Combine dry and wet ingredients

    Slowly stir in almond flour mixture and mix until just combined.

    For this step

    • Dry ingredients
    cookie batter in a bowl with electric mixers coming out
  4. 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 inch apart. Or scoop about a tablespoon using a spoon.

    piping pumpkin cookies on a parchment lined baking sheet
  5. 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.

    two cookies cooling on a cooling rack
  6. 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.

    For this step

    • Butter (softened)
    • Sugar-free powdered sweetener
    • Cream cheese (softened)
    • Heavy cream (if needed)
    mixing a cream cheese frosting with an electric mixer while holding the bowl
  7. 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.

    For this step

    • Two pumpkin cookies (about the same size)
    • Cream cheese filling
    piping cream cheese filling to one side of a pumpkin cookie
  8. 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.

    For this step

    • Chocolate chips (sugar free)
    • Coconut oil
    • Cacao Bliss
    drizzling melted chocolate on top of a whoopie pie in the center

Nutrition

Per serving: 1 whoopie pie

Calories
101
Fat
9.6g
Protein
2.2g
Total carbs
3.1g
Fiber
1.7g
Net carbs
1.4g

Nutrition is an estimate calculated from the ingredients listed. Brands vary, so check labels if you track closely.

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.

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Reviews

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4.8 from 26 ratings, 26 written

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Sonia

I piped the mounds a little bigger than a tablespoon and they came out with a slightly wet center at 12 minutes. Would you leave them in another minute or two, or just let them sit on the pan longer to set up?

Reply

Edith B.

I made a batch of these yesterday afternoon and there are three left. My husband keeps going back to the fridge for them. 🙂

Reply

Dina

I kept waiting for the sugar-free brown sugar to just disappear into the pumpkin, but the molasses note actually holds. That’s what makes it taste like fall and not just pumpkin spice. Two years keto and pumpkin season is back.

Reply

Annie Lampella

The molasses note is exactly why I use the brown here, so glad you caught it!

Reply

Megan

Does anyone know a sub for oat fiber? Can’t find it at my store.

Reply

Annie Lampella

Megan, psyllium husk powder works, just use about 1 teaspoon instead of the 2 tablespoons since it absorbs way more liquid. I’ve also just left it out entirely and added an extra tablespoon of almond flour and they still came out soft.

Reply

Megan

Good tip on the absorption, I’ll start with a teaspoon of psyllium husk.

Reply

Jordan

Squeeze the pumpkin in a clean dish towel before mixing it in. Even 100% pure holds more liquid than you’d think, and I kept getting cookies that spread out flat before they could set, which is annoying when you’re trying to match up sandwiches. Once I started doing that they puffed up like they should, no more digging through a pile of mismatches. Took two batches of sad little discs to figure that out.

Reply

Annie Lampella

Two batches to figure that out, but now you’ve saved everyone else reading these comments. Pumpkin puree moisture varies more between brands than I’d expect. Libby’s runs pretty consistent for me, which is why I never squeezed mine. But I’ve had readers describe exactly those flat cookies that wouldn’t set up right, and I could never figure out what they were doing differently. This was probably it for most of them. If your puree looks wet going in, squeeze first.

Reply

Angela E.

Soft and spiced perfectly, and the filling actually held its shape. Made a double batch after that.

Reply

Annie Lampella

A double batch is smart. I freeze half assembled, sheet pan first so they don’t stick together, then into a bag. Two months easily.

Reply

Angela E.

Oh, the sheet pan step first. Mine all stuck together in the bag and I couldn’t figure out why.

Reply

Danielle

Honestly surprised the texture came out soft and not just dense. The pumpkin spice is way stronger than I expected, so the cream cheese filling is doing a lot of work here.

Reply

Annie Lampella

The pumpkin puree is what keeps it soft. One cup across 24 cookies is just enough moisture without making the batter heavy. I pushed the spice because pumpkin alone is pretty mild, and the filling is what actually saves it.

Reply

Yuki

Mine took closer to 14 minutes, but worth it.

Reply

Annie Lampella

Mine were done at 14 before. Sounds like your oven runs a little hot, Yuki, once you know that it’s easy to adjust.

Reply

Chelsea

1.4g net carbs per cookie. Checked three times.

Reply

Annie Lampella

One cup of pumpkin across 24 cookies, the math just barely holds. Ran it myself a dozen times before I stopped questioning it.

Reply

Tanya

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.

Reply

Annie Lampella

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.

Reply

Tanya

Mine go in the fridge overnight now and I’ve stopped serving them fresh.

Reply

Travis W.

work potluck hero. didn’t even get one myself.

Reply

Annie Lampella

Save one before you even walk in the door next time.

Reply

Crystal

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.

Reply

Annie Lampella

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.

Reply

Aaliyah J.

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.

Reply

Annie Lampella

The caramel-y thing is the milk solids browning. Brown butter and pumpkin spice together, I’m annoyed I haven’t tried this yet.

Reply

Mark

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.

Reply

Annie Lampella

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.

Reply

Dana P.

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.

Reply

Annie Lampella

The quiet second one is the real review. Eight-year-olds don’t fake it.

Reply

Wendy

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.

Reply

Annie Lampella

Baby shower is a tough room. The filling is what gets people every time.

Reply

Rebecca

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.

Reply

Annie Lampella

Oat fiber is carrying this one. Nothing else behaves like it in pumpkin baking.

Reply

Stephanie

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.

Reply

Annie Lampella

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.

Reply

Casey L.

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.

Reply

Annie Lampella

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.

Reply

David Garcia

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.

Reply

Annie Lampella

Scrapers at Easter. Two people who’d normally pass on anything keto cleaning the wrappers is the review I care about.

Reply

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