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.
Marsha says
I have read through all of the comments and realize this is an older post so the information may be someplace else, can these be frozen and reheated? I am the only pumpkin eater in my house.
Carolyn says
Yes, they freeze very nicely.
Pam Sorrels says
This amazing creation of yours is one of the best Keto desserts I have ever had! Honestly just so so fantastic! I will make these over and over again for the rest of my days! Wow! I am in awe. Perfect dozen mesurements and tastes like a naughty muffin that I would spend $5 on and then be miserable. I might just hide them from my children, they are that good! Thanks for all you do and your dedication to making amazing food for us to make and enjoy! Cheers!
Carolyn says
So glad you like them so much!
Delaney says
Are those pepitas I spy on top of the muffins? If so, did you place them before or after oven time? I love being able to give my son stuff like this for quick breakfasts before school–plus, he thinks he’s having dessert for breakfast. Mom knows better. 😛
Carolyn says
In the old version, yes, it had pepitas but most people didn’t even know what they were and I found myself explaining them ALL THE TIME. Anyway, you can just simply press a few on top of the muffins before baking.
rae says
I made this last night. I know a little late to the game, but oh my goodness, YOU’VE DONE IT AGAIN!! These are delicious. Part of me wants to share with family, the other part says, make your own..you’ve all poo poo’d my LC endeavors. Anyway, we will be enjoying these all pumpkin season! Thank you!!
Deb says
Carolyn – do you have to use the protein powder in these? I do not buy protein powder because they all taste so nasty. Any substitute or can it be omitted? 1/4 c might be too much to omit.
Carolyn says
You don’t but… it rises better with it. That said, when you use unflavored protein powder in a recipe like this, you totally won’t taste it at all.
Anonymous says
These muffins were a huge hit at our house!! My husband ate 4 of them and said they were the best muffins I ever made (this from a guy who doesn’t bother if it’s not chocolate!!) My son said they tasted like a cupcake with the frosting inside. Not a single one was left. Thanks for the great recipes. It makes our lo-carb life so much easier.
Carolyn says
Wow, that’s wonderful to hear!
Erica says
Carolyn, thank you so much for posting a video! Usually I skip videos, but was glad for one this time. I made these in muffin top pans (sans cream cheese) and had difficulty determining how many tops to make, because guessing how much a batter will rise while baking is always a crapshoot for me. Seeing how full your muffin cups were was very helpful. My batch is still in the oven, but the batter was delectable!
Erica says
My tops are out of the oven, and they are fantastic! I’m going to make the cream cheese mixture and use it as a spread for them, but they’re great unaccompanied. Thank you, Carolyn. I was able to make 16 3″ muffin tops, in case anyone wonders about doing the same.
Carolyn says
Glad you like it!
Heather says
Has anyone tried these with SF chic chips? I love pumpkin bread/muffins with chocolate chips!
Heather says
*choc chips
Britney says
Can these be made without the whey protein powder?
Carolyn says
Yes but they may not rise as well.
Britney says
I just made the muffins today without the whey powder, I just substituted it with more almond flour, and you’re right they didn’t rise much, but I still thought they were great! I used to love these muffins at Starbucks before I found out I was gluten intolerant, and before I began to follow a low carb lifestyle so it’s great to have a substitute! Thank you 🙂
Carolyn says
Glad to hear it!
Carol Atwell says
I could not go a day without using one of your recipes. Thanks for picking a great one today. LOVE pumpkin this time of year!
Ilana says
This recipe is incredible! My husband, who has had a life-long hatred of pumpkin, loves these muffins. He’s a good sport and has always tasted all of the pumpkin recipes I have made. This is the first one he has ever liked. My daughter and I both love pumpkin and, of course, we love these muffins. I’m planning to make these at Thanksgiving when my grown kids will be here. But I will be making them a lot before Thanksgiving. I have cream cheese softening on the counter so I can make another batch today. Thank you so much for all the wonderful recipes. I’ve made and loved many of them. I’m anxiously waiting the upcoming release of your cookbook.
Sandy @ RE says
Oh Carolyn, these look fantastic. Watching the video, I wish I had these made for breakfast this morning! So glad it’s pumpkin season!
Angela B Mazur-Gray says
Yum! Can’t wait to try these. Think almond milk can be used in place of the heavy cream?
Carolyn says
For the filling? Yes but probably half the amount as it may make it too thin.
Ellen K Stehouwer says
Made these today. Wonderfully delicious! Thank you for another winner!
Carolyn says
Glad you liked them!
Shayna says
What type of liners do you use(I use parchment one now but they pull away from everything and sweat as well) and also what kind of hand mixer do you have? I need a new one that does not splatter stuff everywhere:)
Carolyn says
I use parchment too, that’s what you see here. I use the ones from Paper Chef. My hand mixer is just a cheapie Proctor Silex one.
Louise says
Carolyn I just made these muffins today and they are delicious! Thanks for sharing your recipes with us! I love every one of your recipes I’ve tried so far. Looking forward to trying more! Thank you.
Carolyn says
Thanks, Louise.
Lori says
Carolyn, I have been making these for a couple years now, even in the “off” season! I have taught my 12yo daughter to make them and she does a fine job. We always double them as they go so quickly! I leave the cream cheese out of some for my hubby as he is not a fan, but loves the pumpkin.I also use walnuts on top as I rarely have enough pepitas around. I think we need a batch today!
Carolyn says
Ha I left the cream cheese center out of 6 of these and put chocolate chips in for my kids. They loved them that way!
Michelle Calicchio says
Ok, yum!!!! I think my favorite thing about all of the recipes of yours that I’ve tried is that they’re not super sweet. I love that these are subtly sweet, moist and really delicious! I did not do the topping only because I didn’t feel like going to the store and I needed a good, high-protein snack for the kids before volleyball. These really hit the spot! Both girls won their volleyball games… Coincidence? I think not!
Carolyn says
Haha, yay for the volleyball games. I just updated this recipe RIGHT NOW, as a matter of fact. I skipped the topping and simplified the recipe a bit, so I hope you will come back and check it out!
Theresa Williams says
can Neufchatel cheese be used instead of cream cheese?
Carolyn says
Probably.
Berny says
I tried to check through all previous questions, but this is a popular recipe!!! I’m wondering what is the benefit of allowing the pumpkin to drain on paper towels?? I’ve never seen that before. These alternative flours usually make baked goods so dry anyway, it seems counterintuitive????
Carolyn says
Almond flour is anything BUT dry, as it has a great deal of fat in it, and baked goods made with it can be overly moist. I think you are thinking of other GF flours like rice flour. So drying the pumpkin out a little can really help when working with almond flour..