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 (170.1 g) cream cheese, softened
- 3 tbsp powdered Swerve Sweetener
- 1 tbsp heavy cream
- 1/2 tsp vanilla
Pumpkin Muffins:
- 2 cups (210 g) almond flour
- 1/2 cup (91 g) Swerve Sweetener
- 1/4 cup (27 g) unflavoured whey protein powder, (or egg white protein)
- 2 tsp baking powder
- 2 tsp pumpkin pie spice, (Or 1 tsp cinnamon, 1/2 tsp ginger, 1/4 tsp cloves)
- 1/2 tsp salt
- 2 large (2) eggs
- 1/2 cup (122.5 g) pumpkin puree
- 1/4 cup (56.75 g) butter, melted
- 1/4 cup (62.5 g) water
- 1/2 tsp 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.
Notes
Variations:
Swirled Pumpkin Muffins: Instead of filling the muffins, swirl the cream cheese into the batter top of the batter. Bake as directed.
Plain Pumpkin Muffins: Fill the muffin cups with the batter and bake 15 to 20 minutes. They will bake faster than those with cream cheese. You can also add chocolate chips or chopped nuts.
Storage information:
Store the muffins in a covered container on the counter for up to 3 days or in the fridge for up to 7 days. They can also be frozen for several months.Nutrition
Nutritional Disclaimer
Please note that I am not a medical or nutritional professional. I am simply recounting and sharing my own experiences on this blog. Nothing I express here should be taken as medical advice and you should consult with your doctor before starting any diet or exercise program. I provide nutritional information for my recipes simply as a courtesy to my readers. It is calculated using MacGourmet software and I remove erythritol from the final carb count and net carb count, as it does not affect my own blood glucose levels. I do my best to be as accurate as possible but you should independently calculate nutritional information on your own before relying on them. I expressly disclaim any and all liability of any kind with respect to any act or omission wholly or in part in reliance on anything contained in this website.
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I just made these, and they’re fantastic! You always have the very best keto baking recipes. Thanks so much for sharing these with us.
Got the link for this recipe in my email on 9/3 and made them on Sunday. I did a double batch, filled half with the cream cheese filling and did half with the Pecan crumble that Cheryl spoke of in previous comments. We loved both. Carolyn, I just want to thank you for sharing your amazing recipes with us. I have made many of them and they are amazing.
Excellent!
Wow, these muffins are to die for! You nailed this one for sure! Thank you.
I love these, I added a pecan crumb topping, cuz I love anything I make like a coffee cake????
Pecan crumb topping
1\3 c almond flour
1\4 c Brown sugar
2 TBSP coconut flour
3 TBSP crushed pecans
1 tsp cinnamon
3 TBSP cold butter
Mix til crumbly spoon on top muffins before baking
Feel free to adjust to your liking
I forgot my stars
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I made these pumpkin muffins today, mini muffins, because one muffin is half of my daily intake of carbohydrates as I am normally an OMAD.
These muffins are delicious and moist and perfect for that added snack or dessert.
Don’t know how to share a picture but it’s okay.
Thank you for your recipe
How long did you bake them as minis?!
Thank you so much! These were great. I cut the recipe in half so I wouldn’t be tempted by 12 muffins. I love pumpkin and this was a wonderful first pumpkin bake for me this year.
I wanted to add a word of encouragement to those in Europe (or anywhere else) who do not have access to canned pumpkin. I moved to Europe from America a few years ago and I am ashamed to admit that after more than a few Christmas trips from America I actually filled my checked luggage with many cans of pumpkin. I was talking to my sister who asked me why I don’t just make my own puree and I was somewhat shocked I hadn’t even thought of that. Turns out making puree from a whole pumpkin is easy and it tastes amazing. So for those of you who may not have canned pumpkin access, roasting a pumpkin and making fresh puree is so easy you will kick yourself for not doing it sooner! (and save the seeds for pepitas!
Thanks again Carolyn for another great recipe!
I forgot to add 5 stars to my review so I will put it here 🙂
Thank you!
Made exactly as recipe instructed. So good. Thanks.
Thanks, so yummy!
I want to make these and have on hand Orgain Pumpkin spice protein powder. will this work as a substitiute for the whey protien?
Yes, that should work nicely!
Any idea what the time difference for baking as mini muffins would be? I have a toddler who for sure wouldn’t eat a whole muffin, but would love mini muffins! I cannot wait to try these tomorrow! <3
I am not sure so keep your eye on them!
I swirled the cream cheese in and these are the most beautiful muffins ever. They are still cooling, but we can’t wait to dive in. We like an extra punch of pumpkin flavor, so I added a little of the LorAnn’s pumpkin spice emulsion to it too! Everyone in the house has loved every recipe of yours I’ve made. And since my son’s T1D dx in May, I’ve probably made 25+. I love your book too!
This was easy to do, and so perfect!
The whey protein powder is non-negotiable – perfect amount of batter for 12 muffins!
How do I store KETO PUMPKIN CREAM CHEESE MUFFINS
They’re fine on the counter for 2 days, but the fridge is good for 5.
Has anyone tried freezing these? Thinking of making a double batch.
Yep, they freeze well!
Hi Carolyn! Can you tell me how you stored them for freezing? Plastic wrap vs freezer ziploc etc? I make these weekly for my husbands daily breakfast and snack – but would LOVE to do a double batch and only have to do one time a week!
I put them in big ziplock bags.
As someone who has frozen muffins for decades, I usually bag mine two to a sandwich Ziploc and then double bag all in in a gallon freezer bag. Two reasons, sometimes, when frozen all together, they stick a bit and I only want to pull out one or two. This way, I can make batches of several different flavors and only pull out a couple at a time of any one variety. I also find that double bagging them helps to keep them safer from freezer burn. And of course, the gallon bag gets re-used until it no longer seals! And I’ve learned to take a Sharpie and label them. But maybe things get lost in my freezers more easily then most. Kids have a tendency to move things around on me!
I usually flash freeze mine first. I put them on a platter in the freezer, not touching each other. Once they are solid, I can put them in a freezer bag and they won’t stick together.
I think baking at 350 degrees would work best. I had to add 3+ min to the 25 min at 325.
What kind of pan did you use? And no… keto baking is best at 325, often. 🙂
Hello I have Genpro protein powder will that work in place of the whey
I don’t know what that is. What is the source of the protein?