If you are looking for a delicious pumpkin recipe to celebrate fall, look no further than these keto pumpkin cream cheese muffins. Super moist pumpkin muffins swirled with cream cheese — what could be better?
It seems like every time I go to the grocery store this fall, I wind up with a can or two of pumpkin puree in my cart. What can I say? I’m fully embracing pumpkin spice season this year, and I’m so excited to share my latest keto pumpkin recipe: Low Carb Pumpkin Cream Cheese Muffins.
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These muffins are the best of both worlds — a super moist pumpkin spice muffin base combined with a luscious cream cheese filling. Yum! I love them for an afternoon snack with tea, after dinner for dessert, or even — shh! — for breakfast.
Ingredients in Keto Pumpkin Muffins
To replace traditional grain flours, we’re using a mixture of almond flour and coconut flour in this recipe. I like to use almond flour with a super-fine texture made from blanched almonds. Then, I add a bit of coconut flour. Coconut flour soaks up liquid like a sponge, so we only need to use 1/2 cup in this recipe.
You can use either canned or fresh pumpkin puree in these muffins. I like to use canned pumpkin for its convenience and consistent texture. However, if you’re up for it, you can definitely make this pumpkin bread with fresh pumpkin puree instead.
Easy Keto Pumpkin Muffin Recipe
I hope you’ll try these keto pumpkin muffins. They are scented with warm fall spices and filled with delicious pumpkin flavor. They’re sweet, creamy, a little bit spicy, and incredibly moist. Plus, they’re made with almond flour and coconut flour — so you know they’re low-carb and gluten-free.
Why do I love these pumpkin cream cheese muffins so much?
- They are perfectly spiced.
- They are super moist.
- They are filled with a cream cheese center.
- They keep well in the fridge.
- They are perfect for breakfast, snack, or dessert.
- They make a great dish for Halloween and Thanksgiving.
How to Store Pumpkin Cream Cheese Muffins
I find it’s best to store these muffins in the fridge. And you know, I liked these muffins best served slightly chilled anyway! But, they would also be great at room temperature if you prefer them that way.
Or, you can even freeze these pumpkin muffins. Talk about meal prep!
To do this, remove the pumpkin muffins from the pan and let them cool completely. Either wrap the muffins individually in plastic wrap, or place them in a large “zip” freezer bag.
Make Your Own Pumpkin Pie Spice
Did you run out of pumpkin pie spice? That’s okay, you can make your own! You only need 5 spices to make this homemade version: ground cinnamon, ground ginger, ground nutmeg, ground allspice, and ground cloves — and I bet you already have most of them in your pantry right now.
Simple DIY pumpkin spice mix (yields 1 tablespoon):
- 1 1/2 teaspoon ground cinnamon
- 1/2 teaspoon ground ginger
- 1/2 teaspoon ground nutmeg
- 1/4 teaspoon ground allspice
- 1/4 teaspoon ground cloves
All you need to do is whisk the spices together in a small bowl, and store in an airtight container until ready to use.
If you love these Pumpkin Cream Cheese Muffins, here are some other FALL recipes I know you will love:
Follow me on Instagram and tag #greenandketo so I can see all of the delicious keto treats you are making!
Super moist pumpkin muffins swirled with cream cheese filling. Keto, low-carb, and gluten-free. NUTRITION INFO: Swerve, or erythritol, is a sugar alcohol which is indigestible by humans. It has a glycemic index of 0 (meaning it does not spike blood sugar), and is, effectively, 0 net carbs. All that to say, I count it as 0 net carbs in my calculations. The nutrition information is provided as a courtesy and is approximate only. It was calculated by My Fitness Pal with the recommended brands and ingredients. All brands are different, so please verify the macros with your specific ingredients to ensure accuracy. 
Keto Pumpkin Cream Cheese Muffins
Ingredients
Instructions
Notes
Nutrition Information:
Yield: 12
Amount Per Serving:
Calories: 261Total Fat: 23gSaturated Fat: 11gTrans Fat: 0gUnsaturated Fat: 2gCholesterol: 99mgSodium: 623mgCarbohydrates: 6gFiber: 4gSugar: 2gProtein: 7g
Hello! I don’t see the recipe instructions!!?? I have everything measured and ready, and I just noticed that there are no instructions. Thanks!
Oh, that is so strange that it didn’t save the instructions!
I just updated it now, please let me know how it goes!
Could you use monkfruit sweetener?
Yep, something like Lakanto would work great! Just check the back of the bag to see the conversion.
Mmm these were really good! The batter was very thick and I couldn’t really “swirl” the cream cheese into each muffin too well into the first muffin tin (6 muffins). For the remaining batter I mixed the cream cheese in with an electric hand mixer for the next 6 muffins and that worked better for me. I also sprinkled a little Swerve confectioners sugar on top when they came out of the oven, yum! Pinning your recipe, thanks!
Yes. I found the batter too thick to swirl. I just mucked about with the softened cream cheese on the batter. We’ll see.
Do you know the nutritional facts for this recipe?
What is the serving size in oz? I know it’s per muffin but I made mini muffins out of them so I wanted to do the conversion.
Thank you for the wonderful recipe! Is the nutrition listed somewhere I’m not looking? The recipe pasted in my carb app has them at 15 carbs per serving. I think I’m lost.
Hi Sue,
Hmm, that would be a lot! Sometimes the Swerve can through off the calculators.
My calculator put them at 260 cals, 23g fat, 7g protein, 6g carbs, and 4g fiber. So that’s 2 net carbs per muffin.
Thank you! These look and taste wonderful! Having one now 🙂
Do swerve carbs not count?
Swerve, or erythritol, is a sugar alcohol which is indigestible by humans. It has a glycemic index of 0 (meaning it does not spike blood sugar), and is, effectively, 0 net carbs.
All that to say, I count it as 0 net carbs in my calculations. 🙂
Mine are coming up as 3.7g net carbs, any thoughts ? Can you send a picture of it calculated in your recipe calculator?
My calculator calculated them as being 3.7g net carbs, can you post a screenshot of your recipe calculator results ? Thanks !
Hi Margaret,
Yes, depending on the specific brand of ingredients you use, the calculations could be a bit different.
Mine came out to 260 cals, 23g fat, 7g protein, 6g carbs, and 4g fiber.
And I edited the post to mention that the sweetener I used (Swerve) has 0 effective net carbs. Swerve, or erythritol, is a sugar alcohol which is indigestible by humans.
Hope that helps. 🙂
Thank you! My thoughts are it’s like the almond flour or coconut flour that is to blame for the difference in net carbs, what brands do you use ?
I cant have coconut flour so is there a reason you used both? Would it work it I just used all almond flour?
I haven’t tested this recipe with just almond flour, so I don’t have an exact measurement for you.
Actually your recipe said 623g of carbs..odd and a lot!
What are the net carbs per muffin? I wonder how they would taste without the sweetner also.
Just 2 net carbs per muffin. 🙂 I can’t say what they’d taste like without sweetener, but it you try it, please let me know!
Sarah, I learned a trick somewhere in my years of baking that is really useful, more for cupcakes than for muffins, but both are nice. Spray the paper liners with Pam. Much fewer crumbs sticking to the papers.
Genius, Deb. Thanks for the tip!
I do this all the time!
You are pretty much my favorite person at the moment. I LOVE these muffins. Thank you for the recipe!
Thank you so much, Laura! Glad you enjoyed them!
Did anyone have the batter come out kinda dry looking?
Hi there,
Yes, the batter is a little thick. Scoopable, rather than pourable.
Best pumpkin cheese cupcake ever! My non-keto husband loves them.
Trying these and just want to mention the swerve is confectioners not granulated. May be apparent to all but I was new to making w this stuff.
Hi Colleen,
Swerve comes in both granulated and confectioner’s varieties. This recipe was formulated with granulated. Thanks!
Thank you for clarifying I have one, but not the other – guess I’ll have to go by the granulated one as well – because these look amazing!
I just made these muffins. They’re great. I’ll be making more when these are gone. These will be great for breakfast with a side of fruit. I’ll so make them adding chia seeds and pumkin seeds too.
Can you substitute ground flax for the eggs?
I personally haven’t tried that sub.
Hi Megan, did you end up trying the flax eggs? I was wondering the same thing 😬
Hi Sarah!
These look delicious and I’m eager to try them. I only wanted to verify if you were using salted or unsalted butter for your recipe. Thanks!
Unsalted butter 🙂
I started the recipe and realized that I didn’t have a muffin tin so I improvised and used a bread loaf. I put half the batter added the soft cream cheese then topped it with the rest of the batter.
Instead of 2/3 of a cup of pumpkin are used one cup also are used 16 packets of Splenda in place of the eyrthritol.
My husband who is a diabetic (and a major sugar-aholic) said it was delicious and promptly ate 2 slices.
Thank you so much for sharing.
I’m trying to help is sweet tooth in a more healthy way.
I started the recipe and realized that I didn’t have a muffin tin so I improvised and used a bread loaf. I put half the batter added the soft cream cheese then topped it with the rest of the batter.
Instead of 2/3 of a cup of pumpkin I used one cup…also I used 16 packets of Splenda in place of the eyrthritol.
My husband who is a diabetic (and a major sugar-aholic) said it was delicious and promptly ate 2 slices.
Thank you so much for sharing.
I’m trying to help is sweet tooth in a more healthy way.
You are so welcome — great substitutions!
So which brand of pumpkin purée did you use because every can I see has sugars and a ton of carbs even when subtracting the fiber.
Pretty sure it was my grocery’s store brand. Make sure you’re looking at the plain pumpkin puree, and not the pumpkin pie mix.
Did you use Swerve granular sugar or confectioners sugar?
I used granulated swerve, thanks!
I have these in the oven right now, haven’t tried one yet obviously but the batter tastes awesome! I confess I did add a tablespoon of erythritol to my melted cream cheese and mixed it up till it disolved just to give it more of an “icing ” flavor but other than that I followed the recipe exactly and I already know I’m going to love these. Thank you for posting such a fantastic recipe!
You are so welcome — I’ll add that tip to the instructions 🙂
Can you use stevia or something like that instead?
Hi Lisa,
You should be able to, just check the back of the bag for the conversion. If you don’t mind the slight bitterness stevia can have, it should work.
Hafa Adai (Greetings), from the beautiful island of Guam! Just made the muffins and they are moist and delicious. However, next time, I’d probably add an egg yolk and a bit more swerve to the cream cheese as it wasn’t sweet enough for me. Thank you for this recipe!
Phew!! I thought I was the only one !!!!!
Just made these, they were fabulous, I can’t believe low carb treats can taste so good! I made exactly as directed, but made them in “mini” muffin tins and baked 15 min. Thank you !!!
I’m allergic to coconut does anyone know of any other gods substitute or should I just try using all almond flour?
Did you substitute it and with what because I’m allergic to coconut as well?
Delicious! I said to Hubby that I thought about sweetening the cream cheese, but he quickly said “Don’t mess with perfection!” The only thing I’ll change next time is I’ll be sure to use Philadelphia brand cream cheese. I read on a food blog somewhere that it’s the only one that gets really soft at room temp and creams without lumps, and I have found that to true also. Because my Aldi brand cream cheese wasn’t that soft, I couldn’t really swirl it. Still great though! I love your perfect amounts of sweetener and baking times. Some blogs use way too much sweetener (and I do like it sweet) as if they just took a conventional recipe and changed the flour to almond flour, sugar to Swerve, etc. I appreciate your thoroughly tested recipes.
So is it unsalted or salted butter ? Does it matter ? Also are they mini muffins or regular size ?
Use unsalted butter.
And these are regular size muffins.
Thanks for your comment.
OMGosh! These are incredible! So much more than I expected. Tasty, moist, firm and just all together perfect! So easy and fun to make. My Hubby loves them which makes them even better for me! Thank you for sharing them with us.
You’re very welcome!
Made these tonight but apparently don’t know how to read and so mixed the cream cheese with the butter and sweetener at the beginning. So, no cream cheese swirl topping for me. But the muffin texture was very delicate and fluffy and they tasted great regardless. 🙂
Glad they were tasty!
Made these tonight and they were SOOOOHOOOHOOO good!! Really satisfied my pumpkin cravings. I made them exactly as written and they were perfect. Thanks for the recipe!
Made these and I think I just have over cooked mine the top was a little burnt but I only had them in the oven for 20 minutes so maybe my over is too strong. They ended up tasting like a chemical or something salty even though I followed the recipe. Any thoughts? Mine also looked more brown than the photos I’m going to try again and under bake them.
Hmm, what sweetener did you use?
What would the carbs be if you used coconut sugar?
They’d be about the same as if you used regular granulated white sugar. You can use a calculator like My Fitness Pal to check on the specifics.
So, I have my first batch of these in the oven. HOWEVER, I absolutely HATE the funky aftertaste of erythritol, which is even contained in Lakanto “monk fruit” sweetener. So, I subbed unsweetened applesauce and 7 drops of PURE monk fruit (which is much sweeter). Per muffin the carbs will likely be another 6 carbs or so (I’m guessing between 7-10 net carbs), but a whole muffin is kind of a lot for me anyway, so these will probably be eaten in halves. Either way, fits within my macros. Oh, and instead of using four eggs, I used three and one yolk to balance out the extra moisture of the applesauce. I also subbed applesauce and monk fruit drops to mix with the cream cheese. I will let you know how these turn out!
Can u use silcone muffin pan and not grease?
I haven’t tried that, but it should work out just fine!
I cooked mine for 25min and the toothpick came out clean but the muffin is more of a pumpkin pie consistency once cooled. Is that normal? It taste super yummy but just wondering if I undercooked. Should it come out firm like a muffin? I’m eating mine with a spoon.
Btw this has the best flavor so far in the recipes I’ve tried for pumpkin.
These were so good! Thank you for sharing this! I used allulose, cut down to 1/2 cup and it was perfect!! I only had a giant muffin tin so I made them into 6 muffins… I have to buy regular size muffin tins or I may eat it all!
I made these today, they’re very good!
I used monkfruit for sweetener 1 1/2 tblsp
They were not too sweet something I worry about using
Alternative sweeteners. My batter was very thick so I saved a little batter to fill in after the cream cheese but before I swirled. Also my eggs were huge I lended up with 18 reg. Muffins. Yay more for us!
I’m sorry on the monkfruit I used just a little over 1/3 cups. It turned out just right for me. Sorry for the mistake above. 🤦♀️
No problem, glad you like them!
Just made these, they are so good! Thank you.
Can I sub sweet potatoes for the pumpkin puree.
Yes, I bet you could. But I believe the carb count will be higher.
Thanks for the yummy recipe–just adding another adaptation. Made it in a 7″ push up cake pan in the instant pot. Cooked 44 minutes and then let it self release pressure. Added walnuts to the batter. Of course, it wasn’t crispy like if I used the oven but moist and good texture.
Great, thanks for the note!
Well, what can I say ! Absolutely amazing……. family loved it and I also topped them with a cream cheese frosting divine !
Thank you so much
These are delicious! I must admit I accidentally spaced out and added the cream cheese to the butter in beginning instead of getting to swirl everything before baking but they still came out delicious ! Figured I’d share this in case it helps anyone else in the future . 😀
Absolutely love this recipe and have made it multiple times. I made a few adjustments based on personal preference such as using 4 oz of cream cheese instead of 8 and topping each muffin with 1 pecan before baking. I also really like using Swerve brown sugar replacement for a variation.
I recently moved and can’t find my muffin pan. Can I make this move of a bake? If so, does the baking time change?
Is the nutrients facts just for one muffin or for the whole ingredients ?
Have you ever made them with swerve confectioners I couldn’t find granulated?
Yes, you can.
These are lovely! I am not a baker, but I made them today and they are tasty! Next time I might add a bit of xanthan gum because they were a bit crumbly.
These are lovely! I doubled the pumpkin base because I wanted some with cream cheese and some without. The cream cheese was able to make it on 15/24 of the muffins with an generous dollop, using one 8 oz package. I substituted monk fruit 1:1 and it worked out great. Added a touch of vanilla / pumpkin pie spice to the cream cheese for some added flavor. Overall a great recipe! I also added a sprinkling of pumpkin seeds on the top for a little crunch – yum!
Made exactly as written and oh my goodness! What a perfect Fall treat with a cup of tea. I made 12 full size muffins and 12 mini muffins. I was surprised how thick the “batter” was – more a puree than a batter really. It did not rise at all while baking, which I kept waiting for, but they are soft, fluffy and not at all heavy or dense. They taste of pumpkin for sure. I may add an extra teaspoon of pumpkin pie spice next time. I used salted butter and didn’t need the salt in the recipe.
I am taking some to my mom tomorrow, who just started Keto this week. Thank you for this!
What kind of brand do you use for the canned pumpkin?
Can I freeze these muffins?
I’ve made these twice now and both times they’ve been super delicious. Both times, I’ve added vanilla and caramel extract to the cream cheese mixture.
The second time I made them, I ran out of almond flour so I subbed the additional 1/2 cup of almond flour with flaxseed meal. I honestly like it even more this way!!! The flaxseed adds a nice rustic touch with the pumpkin spice.
I also don’t the cream cheese with the batter since it’s too thick. I just create a tunnel in the centre of the muffin batter, and plop the cream cheese in. The second time I made them, I also added a few Lily’s chocolate chips (Semi sweet) which were a great treat too.
This recipe will be a staple in my arsenal! Thank you!
I really love these and have made them a few times. On reviewing the nutritional information I see that they are 23 grams of fat for 1 muffin, is this correct? It seems like a lot for a single muffin, can you verify that for me please.
Thank you