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.
Sheryl says
I don’t have protein whey. Do you think the muffins would turn out ok without it?
Carolyn says
They may not rise as much but they will taste great!
Lisa says
Ok i swear this is my last comment. We just downed two muffins and my sugar-lovin husband loves them! The first batch i did was overcooked a smidge so be careful of this to anyone interested. This batch with double the spices is seriously sweater weather heaven!
Carolyn says
Wonderful!
Lisa says
Sorry, one more little diddy… i was so mesmerized by the amazing fresh spices that i doubled the amounts plus added nutmeg, too! They are cooling as i write and wow they smell so delicious. I seriously can’t get over how awesome this recipe is.(and all of your other recipes!) Thank you so much for sharing. Your attention to the details make your recipes a step above anything else out there!
Lisa says
Can i ask the difference between almond meal and almond flour? I’m thinking i should know? Also, these are the freakin bomb.
Carolyn says
Almond meal is much more coarse and often doesn’t make as nice muffins.
Annette says
Hi! Can I use almond meal instead of flour? Will it affect the texture?
Carolyn says
Yes, the texture won’t be as good. But if it’s all you have, then you should use it.
Joanna says
My batter is very stiff, is that okay? Did I do something wrong?
What consistency should the batter be?
Thanks
Carolyn says
Low carb, gluten-free batters are always stiffer/thicker than their conventional counterparts, but if it’s too thick to spoon into the pan, you can thin it out with a little almond milk.
Marie says
Wonderful recipe! I did not have any pepitas on hand, so I made a unsweetened coconut/pecan topping instead – and they turned out beautiful. Thank you 🙂
Sally says
No need to apologize. I’ve had some scares with my husband and I know exactly how you feel. Sending warm thoughts and prayers for both of you.
Cindy Litchfield says
Thank you for developing this recipe and sharing it. Thank you also for making it printable.
DANA says
Can you use the green can gelatin instead of unflavored protein powder? Or…vanilla protein powder…?!
Carolyn says
I don’t know if gelatin would work, but the vanilla would be fine. Cut out any additional vanilla.
DANA says
OOOOOPS…just saw this! Thank you!
kwan says
OMG I love these muffins! Ever since i found this recipe A YEAR AGO i’ve been making them every few months. But i do have some little suggestions for anyone about to make these:
1) These take a little long for me to make. To be fair, i am not a natural cook. But if u are planning to make this give yourself about 1hour and a half from start to finish (taking them out the oven). Its not hard to make, just a little long.
2) You absolutely dont have to make/use pepitas. I never did. Muffins still taste amazing.
3) You absolutely do not have to use 8 oz of cream cheese. I use the cream cheese to fill the muffins AND ice the top once its out the oven, and i still never finish it. My family doesnt like frosting so its really only me the puts it on top. Cut the cream cheese in half (so 4 or 5 oz) and use 1 tablespoon of cream instead of 2.
4) It could be sweeter. With just 1/4 cup of sweetner, the end result does taste a little “oat bran” which is sometimes ok with me, other times i want it sweet! I never used Swerve granular, i use Xylitol and i put in a little more than 1/4 cup. So maybe 1/3 to 1/2 a cup. I use 1/4 of Swerve powdered for the cream cheese though.
5) Add nutmeg!! Makes it even more tasty.
I made them last night (12 of them) and only 6 are left. I honest to god love these muffins. This recipe is what made me subscribe to the blog. Even when i’m done with Lyme disease and candida( must eat low carb for both), i will honestly still continue to make these 🙂
Carolyn says
Thanks for all your feedback!
Nikki says
Is the whey protein necessary? Are there any substitutions for this (not protein powder)? I see this a lot in low-carb recipes but it just doesn’t agree with me. TIA!
Carolyn says
The dry protein helps the baked goods rise and hold their shape (a replacement for gluten). So yes, it’s important but you can sub in some egg white powder (just dried, powdered egg whites) instead. You can skip it but they may fall more than normal.
Kelly says
Hi Carolyn! I made these last weekend and they were delicious, however, I had a problem with the muffins “falling” in the center once I took them out of the oven where the cream cheese filling was. Do you think I didn’t put enough batter on bottom and too much on top?
Carolyn says
These are prone to falling a bit anyway, but it might be that they needed a slightly longer cooking time in your oven.
Kelly says
I think they cooked enough, but they fell to the point they were almost hollow on the inside that’s why I was thinking maybe I didn’t put enough batter on the bottom. I was also wondering if adding eggs to the cream cheese mixture might make a difference. thanks-
Carolyn says
Okay, that definitely shouldn’t happen and it certainly didn’t happen to mine. What kind of almond flour did you use? An egg might help but it changes the consistency too.
Kelly says
I use Honeyville almond flour. How much batter did you put on top? I put an icecream scoop worth, so maybe it was just too top heavy?
Carolyn says
I used Honeyville too. I put more batter in the bottom and less on top.
Kelly says
l will try that when I make them again. Regardless of how they looked, they were absolutely incredbly hmmm hmmm good!!
Tamara Gaudet-MacDonald says
I realize you posted this recipe last year, but I had to comment after making these today. I have been searching and searching for low carb, grain free recipes and I feel like the angels are singing! Carolyn, these pumpkin cream cheese muffins turned out so amazing I’m wondering if I’m the one who made them! I followed your recipe to a tee only I used pumpkin pie spice in place of the ginger and cloves as I didn’t have those. My prep time also took longer, but it always does as I am blind and everything just takes a little bit longer. I just want to say thank you for taking the time to share your gifts and your beautiful recipes. I am here forth a dedicated follower. Yours truly…Tamara
Carolyn says
Thank you for your kind words, Tamara! Glad you liked them.
CATRIONA says
OMG these are to die for! I wasn’t sure what you meant by pepitas, since in Spanish that can refer to the seeds of any plant, but assumed it was pumpkin seeds and used those and they tasted delish (ended up eating the leftovers by the handful, haha). thank you for all your recipes, they bring such joy to my life!
Carolyn says
It was pumpkin seeds indeed! I didn’t know that it referred to any seed, that’s great info!
Miranda says
These tasted amazing!!!!
Pam says
I made these today, and they are nothing short of amazing! Truly one of the most delicious LC GF treats I’ve ever enjoyed. I skipped the pepitas (didn’t have any). Thanks for sharing.
MonaKarel says
I use plain pecans. These make wonderful small loaves also
Miranda says
Great idea!!!
Carolyn says
Thanks, Pam!
Jessica says
I was wondering how I’d get by without my Starbucks pumpkin muffin! Now I know!!! 🙂 made these tonight! DELICIOUS!!!
sandi says
Carolyn,
Are whey protein powder and egg white protein powder interchangable in your baking recipes? Thanks in advance, Sandi
Carolyn says
Yes, I think they are. I have used egg white powder in a few recipes and had good results.
sandi says
Thanks for the quick response, Carolyn. I’m going to go make these muffins right now!
tiffany says
I made these yesterday and they are almost gone already! So so so good! I might add in some pumpkin spice or something next time but I’m just starting a low carb diet so I’m probably just still used to super sugary food. These were amazing though.