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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Love your recipes! Thank you! What flour could I substitute for almond flour in your pumpkin muffins? My daughter has a nut allergy. Thanks Carolyn!
Try sunflower seed flour. But you will need to add a little lemon juice to offset the green reaction that happens with baking powder.
Thank you, Carolyn for the recipe. These are delicious!! My family love them. I made a dozen of them in the morning and they were gone by evening, so this time I tripled the recipe. Hopefully I will get more then just one!
Best batch of muffins I’ve made in a while! YUM
Lovely muffin! I used the egg white protein powder as I had just that amount in my bag and wanted to finish it up. The muffins rose beautifully, light and tender texture without the almond flour grittiness that I dislike. Very mild pumpkin flavor. Would have preferred more pumpkin flavor. Next time I’ll try 1 Tablespoon of pie spice to see if I can get a more pronounced pumpkin spice flavor. I feel adding more purée would probably throw off the batter consistency which is perfect as developed. I will also add another tablespoon of sweetener to the cream cheese filling next time as I wanted it to be a bit sweeter. I added a streusel walnut topping which worked out great. Carolyn is a keto baking genius to discover the amazing baking results from the addition of whey protein powder! Thank you!
Great texture and flavor. I used egg white protein powder I had on hand and they turned out great! The only thing I’d change is for them to have a more intense pumpkin flavor. Could have been my pumpkin choice though. I’d definitely make these again!
I made these this morning and they are so yummy. Even though the recipe says to let them cool completely, I couldn’t resist and ate one while it was still warm. My mother didn’t believe these are safe for her to eat and giggled like a little girl when she bit into the cream cheese filling.
thank you for this simple delicious recipe! these muffins were moist and so flavorful! I shouldn’t be surprised, your recipes are excellent and trustworthy. thank you for all the extensive work testing and preparing so we dont have to, much love!!
I made these this week. Interestingly, my recipe (which might have been older) called for 1/2 cup of coconut flour. Was that your technique before using whey protein?
By the time I realized the recipe had changed, it was too late, so I proceeded.
The muffins were pretty good and did not have that grittiness that sometimes coconut flour imparts. But now I’m intrigued and want to try this again with whey protein powder. It will be interesting to compare.
I left the batter alone while I prepared the filling, but when it came to filling the muffin cups, the batter had expanded, and I couldn’t see how the filling would fit.
Still, in the end, the muffins are quite good. I just add a dollop of the filling on top.
Would it be possible to bake this in a bread pan and add the filling in the middle, and swirl it in? How much longer do you think I should bake it if I do this?
Thanks for another great recipe!
This recipe for Keto Pumpkin Muffins has never had any coconut flour. Not sure what you are referring to!
Carolyn….. can you bake it in a loaf pan? If so how long? I want to try this recipe….but might want to make a loaf instead of muffins. It looks so good!
I haven’t tried, but have fun experimenting!
Made a batch and added some pecans. They are awesome!
OMG, these are so great. if I could give you 6 stars I would. I had two of them back to back
I couldn’t believe it. I was never a good baker, but this recipe was easy and again delicious! keep them coming.