Try these delectable keto pumpkin muffins with a rich gooey cream cheese center. They’re a delicious fall breakfast or snack. So good that you might even want to eat them for dessert!
You don’t want to mess with perfection. Take these keto pumpkin muffins, for example. I first posted this recipe back in 2013 and they were a huge hit from the get-go. Readers love them, and my family does too. So we make them every fall.
It’s one of my most popular keto muffin recipes, and with good reason. They have that classic pumpkin spice flavor, with a gooey, creamy cheesecake center. No one can believe they’re sugar free.
They are, of course, modeled after the famous pumpkin muffins from Starbucks. And they taste just as delicious, but with a mere fraction of the carbs.
How does that sound to you, pumpkin lovers???
Why you must try this recipe
In case you haven’t noticed, I am a huge fan of keto pumpkin recipes. There is something so lovely and comforting about the warm spices paired with pumpkin puree.
And these muffins are no exception. They are tender and sweet, with hints of cinnamon, ginger, and cloves. And that sweet cheesecake center takes them to the next level. But if you prefer them plain, I offer instructions for that too!
Best of all, these keto pumpkin muffins have only 3.7g net carbs per serving. Compare that to the hefty 53g of carbs in the Starbucks version.
Other fan favorites include my Keto Pumpkin Cream Pie and Easy Pumpkin Breakfast Bars. And let me not forget my updated Keto Pumpkin Bread, which gets rave reviews every time!
Reader Testimonials
“I made these exactly as written. They were easy to make and tasted fabulous! I can always count on your recipes to be delicious!” — Dana
“These are pure perfection, so delicious! I like extra simple recipes with standard ingredients, and even with the a separate filling, these are simple enough for me to put in regular rotation. I just need to remember to make a double batch next time. Thank you!” — Jamie
“These muffins are the VERY BEST thing I’ve made using Keto ingredients! Thanks!” — Kathy
Ingredients you need
Cream Cheese Filling:
- Cream cheese: Use full fat cream cheese as low fat cream cheese has fillers that can make it higher in carbs.
- Powdered Swerve Sweetener: Use a powdered sweetener for the cream cheese filling so there’s no residual grittiness.
- Heavy cream
- Vanilla extract
Pumpkin Muffins:
- Almond flour: Choose a good, finely ground almond flour for the best texture. This recipe won’t work well with coconut flour, but you can use sunflower seed flour for a nut-free version.
- Swerve Brown: A brown sugar replacement is ideal for the best keto pumpkin muffins. But any granular sweetener should be fine in these, so use what you like best. Do be aware that allulose will make them brown much faster.
- Unflavoured whey protein powder: It’s important to understand the science behind keto baking. Gluten is a protein and in its absence, another dry protein helps baked goods rise properly. You can skip the protein powder, but your muffins will be more dense and fragile. You can also use egg white protein powder instead.
- Pumpkin pie spice: If you don’t have pumpkin pie spice, you can combine ground cinnamon, ginger and cloves.
- Pumpkin purée: You can use homemade or canned pumpkin purée. If it’s on the thinner side, reduce the amount of added liquid.
- Pantry staples: Eggs, butter, baking powder, salt and vanilla extract.
Step-by-step directions
1. Prepare the filling: Beat the cream cheese with the powdered sweetener, cream and vanilla extract until smooth. Set aside.
2. Whisk the dry ingredients: In a medium bowl, whisk together the almond flour, sweetener, protein powder, baking powder, pumpkin pie spice, and salt.
3. Stir in the wet ingredients: Add the eggs, pumpkin puree, melted butter, water, and vanilla extract. Mix until well combined.
4. Fill the muffins: Line a muffin tin with parchment or silicone liners. Drop a spoonful of batter into the bottom of each and use a spoon to make a well in the center. Drop a tablespoon of the filling into the well, then top with more batter to cover.
5. Bake the muffins: Bake at 325F for 23 to 25 minutes, or until the tops are set and the edges are browned. Let cool in the pan.
Expert tips
The filling is optional! I have made these keto pumpkin muffins several different ways. I love the filled muffin style, but I have also swirled the cream cheese into the top of the batter (very pretty!). And I’ve made them with no filling at all!
So if you prefer a classic pumpkin muffin, feel free to skip the filling. Adding chopped nuts or chocolate chips is delicious too.
The rise and fall of keto pumpkin muffins: If you do make filled muffins, expect them to rise nicely and then sink a bit as they cool. That is the nature of cream cheese stuffed goodies. The filling expands during baking, and then contracts as it cools. So a little sink hole will appear in the tops of the muffins. They still taste fabulous!
Dairy-Free Option: You can make these muffins dairy-free as well, with egg white protein powder, dairy-free cream cheese, and coconut cream. Replace the butter with your oil of choice and enjoy!
Frequently Asked Questions
Canned pumpkin puree has 12g of carbs and 4g of fiber per half cup serving. While it’s not the lowest carb option, it can be consumed on a keto diet in small quantities. This keto muffin recipe uses only half a cup spread out over 12 servings, so it’s very keto-friendly.
This keto muffin recipe has 6.1g of carbs and 2.4g of fiber per serving. That comes to 3.7g net carbs per muffin.
This keto pumpkin muffin recipe was developed and tested using almond flour. However, you can use sunflower seed flour as a 1 to 1 replacement. Just remember to add a tablespoon of lemon juice to offset the reaction between sunflower seeds and baking powder. They will turn a lovely shade of green if you forget!
More recipes you might enjoy
Keto Pumpkin Muffins Recipe
Ingredients
Cream Cheese Filling:
- 6 oz cream cheese softened
- 3 tablespoon powdered Swerve Sweetener
- 1 tablespoon heavy cream
- ½ teaspoon vanilla
Pumpkin Muffins:
- 2 cups almond flour
- ½ cup Swerve Sweetener
- ¼ cup unflavoured whey protein powder (or egg white protein)
- 2 teaspoon baking powder
- 2 teaspoon pumpkin pie spice (Or 1 teaspoon cinnamon, ½ teaspoon ginger, ¼ teaspoon cloves)
- ½ teaspoon salt
- 2 large eggs
- ½ cup pumpkin puree
- ¼ cup butter melted
- ¼ cup water
- ½ teaspoon vanilla extract
Instructions
Cream cheese filling
- Beat the cream cheese with the powdered sweetener, cream and vanilla extract until smooth. Set aside.
Muffins:
- Preheat the oven to 325ºF and line a muffin tin with parchment or silicone liners.
- In a medium bowl, whisk together the almond flour, sweetener, protein powder, baking powder, pumpkin pie spice, and salt.
- Add the eggs, pumpkin puree, melted butter, water, and vanilla extract. Mix until well combined.
- Drop a spoonful of batter into the bottom of the prepared muffin tins and use a spoon to make a well in the center of each. Drop a tablespoon of cream cheese filling into the well, then top with more batter to cover.
- Bake 23 to 25 minutes, or until the tops are set and the edges are just browned. Let cool completely in the pan.
Danielle says
First time making these last night, they were outstanding! My son, who is a chef, said they were the best low carb version of anything we’ve ever made. Also, my first time working with Swerve, which I think is an outstanding sweetener. I finally located it at our Whole Foods that recently opened, and I used a coffee/spice grinder to powder it for the cream cheese filling. Again, just a really outstanding recipe, thanks so much for sharing!
Carolyn says
Wow, that is high praise. So glad your son liked them too!
nicole thomas says
so impressed caroline!! absolutely delicious and beautiful….. by far my favorite so far! thank you so very much for all you do for all of us!
nicole thomas says
oops! i’m so sorry for misspelling your name carolyn…. everyone always puts an “h” in mine!!! caroline or carolyn, what your real name should be is wonder woman!!!
Carolyn says
It’s okay, so many people call me Caroline, it rarely phases me 😉
Liz says
These are hands-down the best low carb pumpkin muffins of any low carb cooking site. We’ve tried many recipes and these are fabulous! Thanks very much!
Carolyn says
You’re welcome.
Tania P. says
I have made several of your wonderful recipes and passed your blog along to my friends. These yummy muffins are my favorite so far followed by the orange cardamom biscotti . It’s nice to be able to enjoy something besides “meat and eggs” with my morning coffee
Carolyn says
I agree, it is so nice not to just rely on bacon and eggs in the morning!
MarciaH says
I have serious kidney issues and I’m always trying to reduce the protein and phosphorus content of food I eat (in addition to restricting carbs). It makes for a walk through a minefield. I have already had to replace the baking powder (wicked high in phosphorus and pepitas–also very high). What’s left is to ask you about 2 ingredients in this: eggs and whey powder. Egg whites are low in phosph. but the yolks are high. And whey protein is also high. Could the whole eggs be replaced with just the whites? Is there something that can sub for the whey powder? Since I don’t know exactly what its function is, I can’t answer the question for myself. Thank you for all your great recipes. I wish I weren’t so limited in what I can eat.
Carolyn says
Hi Marcia…okay, go for 3 egg whites and for the whey powder, you can use either egg white powder (sometimes called meringue powder) or hemp protein (don’t know if that’s lower in phosphorus. For the baking powder, you can sub baking soda and cream of tartar, do you have that?
The whey protein is to replace the gluten. Gluten is a protein so adding protein helps things rise and hold their shape properly!
MarciaH says
Thank you. I do have the baking powder sub. Do you think psyllium could sub for whey? I use it in a lot of other low carb baking to hold things together. There is very little info about hemp on the Internet. What I found says that 100grams is the equivalent of 1 whole egg (in phosph), so that’s not too bad. Would it sub 1:1 for whey?
Carolyn says
i’ve never used psyllium so I can’t say. But these sink a little in the middle anyway, because of the cream cheese filling. so I say go for it!
Megan says
Hi Ms Carolyn 🙂 I’ve just started my foray into a gluten free world due to my recently discovered non celiac gluten sensitivities, but I’ve been low carb for many years. Your website has been a godsend. I made these last night and they were fantastic, out of the 16 I ended up with there are 3 left…husband and kids loved them too! For our families tastes I will add a bit more pumpkin next time and some more erythritol in both the cream cheese filling and pumpkin muffins…but this was just a great, great recipe. Thank you for all you do!
Carolyn says
Thanks, Megan!
Jen says
Hi Carolyn. Another great recipe! I left the topping off but that’s okay they are still delicious! I make these for my breakfast. I just pop one in a baggie everyday and take it to work with me. They are super yummy! Thanks.
shawn krosnick says
These were amazing…. and I even messed up the recipe and they still came out great!! I didn’t have enough almond flour and used extra vanilla whey protein… Still wonderful. Thanks for the wonderful recipes!!!
Deborah says
made these today and they are *insanely* good. thank you so much!!!
Carolyn says
Glad to hear it!
LaRaine says
These muffins are delicious!!!! I didn’t have whey protein powder, but did have hemp protein powder, so I used it. I will most definitely make them again and again!! I refrigerated them after cooking because of the cream cheese – is that necessary?
Carolyn says
They are okay on the counter for a day, but after that, definitely in the fridge. Glad you liked them!
Mona Karel says
This is becoming my most requested cake. I’ve made it as muffins, mini muffins, and recently as small loaf cakes. I put raw pecans on the top instead of the candied pumpkin seeds. MMMMMMMMMMMMMMM
I’ll be sharing on my blog. THANKS
Manda says
OH MY!!!! Me and my daughter made these last night. Easily the best pumpkin muffin recipe I have made lately. I started my venture of low carb, gluten free, sugar free in march and am so glad I found your site. I have made several of your recipes and am ways happy with the results. Keep up the excellent work.
Carolyn says
Thank you, Manda!
Marianna says
I’ve now made these muffins twice and they are so delicious! Thank you so much for the recipe! I hope your husband’s recovering is going smoothly!
Carolyn says
Thanks, Marianna. He’s doing well!
Mia says
I’m praying for your husband’s recovery, and for you and your family to be strengthened during this time. Thank you so much for this amazing recipe! I haven’t tried Starbucks’ pumpkin cream cheese muffins, but I’ve discovered Whole Foods’ has a yummy version. Knowing I want my family to enjoy a healthier version, I searched your website and found just what I was looking for. I can’t express the sheer joy I felt when I discovered you had just posted this one. An answer to prayer for sure! Yours is one of my favorite blogs!! Thanks for all you do in creating and sharing your wonderful recipes! You’re a blessing to my family for sure!
Carolyn says
Thanks for your kind words, Mia.
Lady Jennie says
Oh wow! I just came for a pumpkin recipe!
So so SO glad your husband is okay.
Carolyn says
Thanks, Jennie!
Dana says
Any idea if substituting a collagen protein instead of whey would work ok?
Carolyn says
No, it won’t. It makes things gummy and hard to cook through.
Michelle H says
I just made these right now. I used whole milk instead of almond milk, and Splenda instead of the other sweetener. The cream cheese filling is easily the best part, so I’m glad I used a lot in each muffin. The muffins, on their own, tasted like almonds, from the flour, but combined with the filling….awesome. They got a big thumbs up from myself AND my husband. They’re definitely going on the “when I feel like baking I’ll make…” list! Thanks for the recipe!
Carolyn says
Hi Michelle, glad you like them. What kind of almond flour did you use? Because the really fine, blanched stuff (like Honeyville) typically doesn’t have much almond flavour when baked.
Michelle H says
I didn’t, it was Bob’s Red Mill which is what my local store had. Next time I make them I’ll try something else.
Carolyn says
Bob’s is pretty good, but a little coarser than Honeyville so that may have been part of it.
Tessa says
Prayers for your husband and you! Glad he’s going to be okay though.
If you need any more suggestions for Makeover Monday, I would love a low carb version of Aussie Bites. Costco got me addicted to these convenient little gems, but lately I’ve been denying myself because of the carbs. There are recipes galore online to make the original version (with oat flour) and I did find one that used a tiny bit of coconut flour but it was still mainly oat flour. You would forever be my hero if you converted this!!
Love your site!
Carolyn says
Ummmmm….never heard of them. Can you send a link to a good recipe?
Tessa says
Sure thing. Here actually are 3 links (you’ll see why):
This I think is the original recipe (containing wheat) that usually comes up all over the web when searched: http://bad-girls-kitchen.blogspot.com/2008/06/aussie-bites.html
Then Costco went to using just oat flour so they were gluten free (in theory anyway) – and now for the life of me I can’t find any recipes using just oat flour although I know I’ve seen it before!
This is the one “adapted” recipe where some of the oat flour was replaced with coconut flour: http://www.consciouseatery.com/2012/11/allergy-free-aussie-bites.html
I did just stumble across this one while searching where they use almond flour but there’s still a lot of oats in there: http://www.keyingredient.com/recipes/616033599/aussie-bites/
Hope I haven’t overwhelmed you!!
Carolyn says
Okay, I will add that to the To-Make list!
Tessa says
Awesome! Thanks!
Ivonne Carlo says
OMG I’m so sorry about your husband’s accident. I’m glad he’s alive and getting the care he needs to be 100% again. And you are one admirable woman posting recipes even with all that going on. You have my full respect! xo
Carolyn says
Thanks, Ivonne. I had you in mind when I made this recipe!
Nancy Ceresia says
Oh Carolyn! I spied the link in my email earlier this week and was really excited to check it out – Could my dreams of enjoying a pumpkin cream cheese muffin once again come true? But I only got around to checking out the full post last night and I was blown away. Wow, what a post!! So glad you are all ok – that is, as ok as you can be, considering. I am amazed at your resilience. That and your dedication and creativity will get you through, I have no doubt. Thanks for taking the time to read comments. 🙂 I think it was mine that I left a couple weeks ago about these dreamy muffins, so was thrilled to see them materialize, if not only virtually for the time being. Best wishes. Nancy
PS – Are you connected with Lynn Terry? She is a big low-carb lifestyle blogger: http://www.travelinglowcarb.com/ She is a genuine, authentic person like yourself. 🙂
Carolyn says
Was it you, Nancy? I couldn’t remember who asked for these! Glad you like them. And now, I don’t know Lynn but I will be sure to check out her blog!
Christopher says
Is there a substitute for the protein powder? I have everything slse
Carolyn says
You can skip it but it really gives better consistency and better rise.
Leslie Preston says
Many wishes for a speedy recovery for your husband. I’ve now run into (sorry) three people who had extensive ankle surgery, they all recovered beautifully, AND all were probably twice as old as your husband! One man said that instead of crutches, he used one of those things where you kneel on something like an elevated scooter-type thing to get around, so non-weight-bearing. Also, isn’t it something how an accident like this suddenly slaps everything into perspective?
I love your blog! I’ve made many of the recipes and then have turned around and blabbed and blabbed to family/friends on how they can cut out the sugar in their lives and still be happy/satisfied. AND, I’ve been reading these comments to you and think what a great group of people follow your blog! It’s a win-win all over the place!!!
Carolyn says
Thanks, Leslie. Yeah, I saw those scooters and thought they might not be a bad idea. My husband is 6’7″ though, so we need to make sure whatever we can can accommodate his height. He has crutches from a previous leg injury so at least we have those!