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Keto Pumpkin Cupcakes

Annie Lampella, Pharm.D. Recipe developer and pharmacist

Published Updated

31 ratings

Tender pumpkin cream cheese muffins — brown-buttered keto pumpkin spice cake under a tangy frosting, 4.5g net carbs each. I've been baking these every Fall since 2018.
  • 4.5gnet carbs
  • 5.1gprotein
  • 28minutes
  • 16servings
beautiful Fall inspired cream cheese topped pumpkin muffin
muffins on a wire rack with frosting on them
a bite taken out of a pumpkin muffin
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I make these every Fall, and they're one of the few pumpkin recipes where my family doesn't even realize they're low carb. The secret is brown butter. It adds a nutty, almost caramel-like depth that regular melted butter can't touch, and it pairs with the pumpkin spice in a way that makes these taste like something from an actual bakery.

Keto pumpkin muffins topped with cream cheese frosting rosettes

At only 1.4 net carbs per muffin, I don't think twice about grabbing one with my morning coffee. The base uses a mix of almond flour and coconut flour, which I've found gives you the closest texture to regular flour. I tested both individually early on. Almond flour alone was too heavy; coconut flour alone was too dry and crumbly. The combination finally gave me the spongy, tender crumb I was going for.

The frosting is what pushes these over. It's tangy enough to balance the sweetness, and the whole thing reminds me of the filling in my pumpkin roll. If you're a fan of pumpkin cheesecake, you'll love what it does here. I pipe mine with a star tip, but you can also poke a hole in the center and fill the muffin before piping on top.

I add turmeric to the spice mix, and most pumpkin recipes skip it entirely. It's the ingredient people can never quite place when they taste these, but it rounds out the cinnamon and nutmeg in a way that just works. I've been tweaking this ratio since 2018, and this is the combination I keep coming back to.

One thing I learned the hard way: the frosting weeps if you leave it on overnight. I frost right before eating and store the cream cheese mixture separately in the fridge. The muffins themselves hold up for about 3 days unfrosted. Reader Sarah figured out the same trick on her own, which told me it wasn't just my kitchen being weird.

If you're in a Fall baking mood, my pumpkin dump cake and cinnamon coffee cake have the same warm spice profile. And for a faster pumpkin fix, the pumpkin mug cake takes about 2 minutes in the microwave.

Baked pumpkin cupcakes cooling on a wire rack.

Is pumpkin keto friendly?

Pumpkin is absolutely fine on keto. Yes, it’s a squash and it’s higher in carbs compared to other low carb vegetables, but there are only 7 net carbs in half a cup of pumpkin puree.

This recipe uses 1.5 cups of pumpkin puree split across 15 muffins, which works out to just 1.4 net carbs per muffin. I did that math early on because I wanted to make sure I could eat two without second-guessing it. Totally worth it for real pumpkin flavor during Fall.

How I make the frosting

The sugar-free frosting is the easiest part. I whip softened butter and softened cheese with vanilla and powdered erythritol until it’s fluffy, then pipe it on. You have a couple of options:

  • Pipe on top using a star tip or whatever piping tip you prefer. This is how I usually do it.
  • Fill the center by poking a hole in the top of the muffin, piping frosting inside, then covering the hole with more on top. Think of it like a filled mini cheesecake situation.
Two frosted cupcakes next to each other with a cinnamon stick nearby.

What if I skip the frosting?

I get asked this a lot. The muffins are great on their own if you want something lighter, and the macros shift a bit. Here’s what one unfrosted muffin looks like:

Calories: 162
Fat: 12.7 g
Net Carbs: 4.3
Protein: 4.1 g

I sometimes eat them plain during the week and save the frosting for weekends when I want the full experience.

Storage and freezing

Store unfrosted muffins in an airtight container at room temperature. They stay fresh for about 3 days. After that, sugar-free sweeteners tend to dry baked goods out faster than regular sugar because they don’t hold onto moisture the same way.

To freeze, wrap each unfrosted muffin individually in plastic wrap, then put them all in a freezer bag. They keep for about 2 months. When I want one, I pull it out the night before and let it thaw in the fridge, then frost it fresh in the morning.

I don’t freeze them with the frosting on. It changes the texture and you end up with a watery layer on top once it thaws. Keep the frosting in a separate sealed container in the fridge (it lasts about a week) and pipe it on fresh.

How to make these pumpkin muffins

The brown butter is the step that makes the biggest difference here, so don't skip it. Heat the butter until the milk solids turn golden and the whole pan smells nutty (about 5 minutes). Then let it cool before adding it to the batter. If you pour it in hot, you'll scramble the eggs.

For the batter, mix just enough to get it smooth. I used to overmix mine and the muffins came out dense every time. Once I started folding the dry ingredients in gently, the texture changed completely.

Close up of a pumpkin cupcake topped with creamy cream cheese frosting.

Key ingredients and substitutions

  • Brown butter adds a nutty warmth that pairs with the earthy pumpkin spice. Regular melted butter works in a pinch, but you lose that toasted flavor.
  • Almond flour + coconut flour together mimic regular flour. If you have a nut allergy, try sunflower seed flour in place of the almond flour.
  • Spices (cinnamon, turmeric, nutmeg) give you classic pumpkin spice flavor. You can substitute 2 teaspoons pumpkin pie spice if you want one jar instead of three.
  • Sugar-free maple syrup adds a subtle maple note. If you don't have it, add an extra 1/4 cup brown sugar-free sweetener instead.

The cream cheese frosting is similar to what I use on my hostess cupcakes, just without the chocolate. Whip it until fluffy and pipe it on with whatever tip you like.

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The recipe

Keto Pumpkin Cupcakes

Print Pin
Prep 8 min Cook 20 min Total 28 min Serves 16

Ingredients

Servings 16

Keto Pumpkin Cupcakes Ingredients

Keto Cream Cheese Frosting Ingredients

Step by Step Instructions

  1. Preheat oven

    Preheat oven to 350 degrees. Line a muffin tray with muffin liners.

    350 red letters on the oven

  2. Make brown butter

    Heat butter in a small saucepan over medium heat. Cook the butter, swirling occasionally, until the butter has melted, starts to brown and smells nutty (about 5 minutes). Remove from the heat and set aside to cool.

    For this step

    • 1/2 cup unsalted butter
    melted brown butter in a saucepan

  3. Mix dry ingredients

    In a medium bowl, whisk together flours, baking powder, baking soda, salt and spices. Set aside.

    For this step

    • 1 1/2 cups almond flour
    • 1/2 cup coconut flour
    • 2 teaspoons baking powder
    • 1 teaspoon baking soda
    • 1 1/4 teaspoon salt
    • 2 teaspoons cinnamon
    • 1/2 teaspoon turmeric
    • 1/4 teaspoon nutmeg
    mixing together dry ingredients with a whisk

  4. Mix wet ingredients

    In a large bowl, beat the eggs, pumpkin, golden monkfruit and syrup until smooth.

    For this step

    • 1 1/2 cups pumpkin puree
    • 3 eggs
    • 1/4 cup brown sugar free sweetener
    • 1/2 cup sugar free maple syrup
    mixing wet ingredient and pumpkin with an electric mixer

  5. Combine all

    Mix in the dry ingredients along with the browned butter.

    keto pumpkin muffin mixture in a glass bowl

  6. Bake

    Pour into a muffin pan lined with muffin liners. Bake at 350 degrees for 20-25 minutes or until they start to brown on top. Remove from the oven and let cool completely before frosting.

    pumpkin muffin batter in a muffin pan

  7. Cream cheese frosting

    To make the cream cheese frosting, add cream cheese, butter and vanilla to a medium bowl. Whip until fluffy and smooth. Slowly add in the powdered erythritol and mix until fluffy. Spread or pipe on top of each cupcake. You can poke a hole in the top of the cupcake to insert the cream cheese frosting into the center of the cupcake.

    For this step

    • 8 oz cream cheese, softened
    • 1/2 cup unsalted butter, softened
    • 1 teaspoon vanilla extract
    • 1/2 cup powdered sugar free sweetener
    piping cream cheese frosting on a pumpkin muffin

Nutrition

Per serving: 1 cupcake

Calories
262
Fat
23.2g
Protein
5.1g
Total carbs
13.3g
Net carbs
4.5g

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

Frequently Asked Questions

Can I bake this in a loaf pan instead of muffins?

I've done it. Use the same temperature (350 degrees) and bake for 40 to 55 minutes. The center takes a lot longer to set in a loaf pan, so I check it with a knife around the 40-minute mark. When the knife comes out clean, it's done. Let it cool completely before slicing or the center will be gummy.

What can I substitute for sugar-free maple syrup?

I'd add an extra 1/4 cup of brown sugar-free sweetener in its place. You lose the maple note, but the pumpkin spice carries the flavor on its own. I've made it both ways and my family didn't notice the difference.

Can I freeze these muffins?

I freeze them all the time. Wrap each muffin individually (unfrosted) in plastic wrap and store in a freezer bag. They're good for about 2 months. I thaw mine overnight in the fridge and frost fresh the next morning. Don't freeze them with frosting on, or it gets watery when it thaws.

Why does the frosting get watery if I leave it on the muffins?

The moisture from the muffin slowly migrates into the frosting and makes it weep. I noticed this after leaving a batch frosted in the fridge for two days. Now I store the frosting in a separate container and pipe it on right before eating. The muffins last longer this way too.

Can I use pumpkin pie spice instead of individual spices?

Yes. I use 2 teaspoons of pumpkin pie spice when I don't want to measure out three separate jars. The result is close enough that I can't tell the difference in the finished muffin. I still prefer my own mix (cinnamon, turmeric, nutmeg) because the turmeric ratio is higher than what's in most store-bought blends.

Can I make these nut-free?

I'd swap the almond flour for sunflower seed flour, same amount. The batter might look slightly green from the sunflower seeds reacting with baking soda (it's a chemical reaction, totally harmless), but the taste is the same. I've tested this swap for readers with nut allergies and it works.

How do I keep the muffins from turning out dense?

I had this problem for my first few batches. The fix was mixing less. Fold the dry ingredients into the wet until just combined. If you beat the batter too long, you knock out the air bubbles and the muffins come out heavy. Also make sure your baking powder isn't expired. Old leavener is the silent killer of spongy texture.

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Reviews

Tap to rate

4.8 from 31 ratings, 19 written

Made this recipe?

Replying to Luz

Your rating

Sam W.

I’m still pretty new to keto (two months in) and this was my first time baking anything with almond and coconut flour, so I followed every step really carefully because I didn’t want to ruin them, and the batter looked weirdly thick before it went in but the muffins came out way better than I expected. Good texture, surprisingly. The nutmeg in the spice mix really comes through, and the cream cheese frosting has just enough tang to keep things from getting too sweet. Didn’t think keto baking could pull something like this off.

Reply

Annie Lampella

That thick batter threw me too the first time. Coconut flour absorbs way more than regular flour, so it always looks off before it goes in. Glad the nutmeg came through – I almost cut it in the first version.

Reply

Natalie

Do I need to brown the butter or can I just melt it? I’ve never done that before.

Reply

Annie Lampella

You can just melt it and it’ll work fine. What you’re giving up is that nutty, toasty note the browning adds. Pumpkin spice is punchy enough here that you won’t miss it. If you want to try browning it, use a light-colored pan, watch it close, and pull it the second the foam clears and it smells nutty.

Reply

Diane

The turmeric is doing more than just color here. I bumped it to a full teaspoon and the whole spice blend has this warmer, earthier backing note that makes the cinnamon land differently.

Reply

Annie Lampella

Turmeric was always doing more than color here, I just never pushed past the half teaspoon. That cinnamon shift is what’s going to make me try a full on the next batch.

Reply

Donna

Thought pumpkin was a hard sell at a dinner party. Empty tray.

Reply

Annie Lampella

Thank you for telling me, Donna! An empty tray is my favorite kind of review, and that cream cheese frosting is what usually flips the pumpkin skeptics.

Reply

Sasha

My oven’s been running hot and I’ve already ruined a couple batches because of it. Making these for a get-together this weekend, so wondering if an air fryer would work. Would I need to go lower than 350 and pull them earlier than I would in a regular oven?

Reply

Annie Lampella

Yeah, air fryer works. I’d go 325 and check at 12 minutes. The tops brown fast in there, so use a toothpick, not just color.

Reply

Rachel

Brown the butter. I skipped it once thinking it probably didn’t make a difference and I was wrong.

Reply

Annie Lampella

It carries the whole flavor. Nothing in the spice blend lands the same without it.

Reply

Angela

Came back to keto this spring after months off track and this was the first thing I made. I forgot what it felt like to eat something sweet and actually feel okay about it. The brown butter smell while it’s mixing is something else, and the cream cheese frosting is so good I had to stop myself from eating it straight. This recipe is the reason I’m not going anywhere.

Reply

Annie Lampella

Frosting straight from the bowl, every single time I make these. No regrets.

Reply

Sonia

Fourth batch since I found this recipe, which for a pumpkin muffin in April says something. Don’t skip the brown butter; you can actually taste it in a way regular melted butter doesn’t. Frosting could go tangier, but minor.

Reply

Annie Lampella

Four batches in April, I’ll take it. For tangier frosting, a teaspoon of lemon juice does it. Small but you’ll notice.

Reply

Donna P.

These are so good that I’m a little annoyed at myself for waiting until March. Had a can of pumpkin puree in the pantry and figured why not, and now I totally get why people lose their minds over fall baking. The brown butter step makes a difference you can actually smell — the whole kitchen shifts the second it starts to turn. One thing though: the frosting felt short for 16 muffins. I ended up making a half-batch more to cover them all, which wasn’t a hardship, just something to know going in. Four stars for the cake, which was everything.

Reply

Annie Lampella

Yeah it’s a light-coverage batch by design. I do 1.5x whenever I want full swirls on all 16. And yes, that’s the exact moment on the brown butter. Once the smell shifts you have maybe 30 seconds before it crosses over.

Reply

Sarah

Double batched these on Sunday and now I’m annoyed I didn’t find this recipe sooner. Keeping the cream cheese frosting in a separate container and topping fresh, because it gets watery by day two if you leave it on the cupcake. These are going in my weekly Sunday batch from here on out.

Reply

Annie Lampella

Yeah it weeps fast once it sits on top. I frost right before eating too. The cupcakes hold up through the week unfrosted, so it’s worth the extra step.

Reply

Luz

the frosting is legit

Reply

Annie Lampella

The cream cheese cuts through the sweetness just right. I added a tiny bit of cinnamon to mine last batch.

Reply

Janette

This recipe is the bomb. I’ve made a number of keto dessert recipes, many good, but this is a fast family favorite. Thank you!

Reply

Annie Lampella

Love that it became a regular one for you. The spice mix does most of the work here.

Reply

Julie

Hello Annie, I have been a long time follower and have made many of your recipes but I just found this one (I don’t have a sweet tooth) and this one is also a keeper. Thank you. Happy Halloween! Julie

Reply

Annie Lampella

The brown butter is why, I think. Gives these a nutty depth that keeps them from tipping into full dessert-sweet. Glad you found it.

Reply

karin mickelson

Is there another option or substitute for the no sugar maple syrup?

Thank you!

Reply

Annie Lampella Recipe author

You can add more brown sugar free sweetener instead. Maybe another 1/4 cup.

Reply

Ginevra

Thank-you, I just came to the comments to ask that question because I can’t have maple and was wondering if I could just leave it out.

Reply

Dana S

I realize I’m a year behind this recipe, but I’m interested in making this in a loaf pan. Do you know if this recipe will fit into 1 loaf pan? Temperature and timing?

I love watching your YouTube videos!

Reply

Annie Lampella Recipe author

I haven’t tried it in a loaf pan, but I would bake at the same temperature for longer. Maybe 40-55 minutes. Bake until it is set on top or you insert a knife in the center and it comes out clean.

Reply

Lorraine

One of the BEST muffin (even cupcake) keto recipes I have tried! Long time internet keto recipe maker, first time reviewer. They are that good.
Perfect for the holidays for my husband and I to indulge while the rest of the family eats pie and whatever else. Will be making these all year!
Thank you!! 🙂

Reply

Annie Lampella

First time reviewer after years of keto cooking, I’ll take it. I double batch these for Thanksgiving and eat three while everyone else has pie.

Reply

Brandi

I think this is my 3rd time making these. I thought I have left a comment before… Just wanted to say these are so yummy and I want to try some more of your recipes. I will say, it’s hard to tell when the muffins are done in the oven because they stay pretty dense and wet in the center, but once they have been refrigerated they seem fine. I kept mine in the oven a bit longer than stated. My two year old loves them too 🙂

Reply

Annie Lampella

Yeah the pumpkin puree keeps them wetter longer than most muffin recipes. Toothpick won’t tell you much here. I go by the top not being tacky when I press it gently and the edges just barely pulling away. They firm up a lot overnight in the fridge.

Reply

Kathy

Absolutely AMAZING ! I haven’t tried any of your recipes that weren’t wonderful, but these are the best so far !

Reply

Annie Lampella

Brown butter is what makes them. Worth the extra five minutes.

Reply

Dawn

Best way to put this is Heaven! I love these so much.

Reply

Annie Lampella Recipe author

Hi Dawn! I am glad you liked it! And thank you for all of your positive comments throughout my recipes! They always make my day! Annie

Reply

deborah dunstan

Can you tell me the total sodium per cupcake please and thank you?

Reply

Annie Lampella Recipe author

They are about 275 mg per muffin.

Reply

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