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.
Beth says
these are the best pump cream cheese muffins. They are easy fix and never disappoint. They are so good, I always make a double batch so Ai have some in the freezer and some to share with my pumpkin spice friends.
Lynnette says
I made these for dessert tonight and they very food. I will make them again. Loved the idea of the cream cheese filling it was an extra surprise. Thank you, Caroline, for all you put into this website.
Lynne Spence says
Oh my, these are amazing!!! Yes, I know it’s Spring and I really did plan to make something more “Springy”, but I found a can of pumpkin in the pantry that was begging to be used. These are sooooo good, I will definitely be making them again!!
Rona says
I just keep coming back to this recipe, which is soooooo good, so thanks for sharing!!! just some notes for silent readers- i used banana flavoured protein powder and it didnt affect the flavour, and i put these spices cause i dont have the blend: cinnamon as the ratio written in the recipe, grounded cardamon, and a pinch of white grounded pepper, i also have a spice that is made from the inside of cherries seed, dont know how you call it, in my country its called mahleb, so a bit of that too , sometimes i add nutmeg and a tiny bit of cloves. after making the cheese blend i freeze it in plastic wrap rolled as a long tube so its easier to cut when the dough is ready. I really appreciate the sharing❤️
Carolyn says
Thank you!
Elizabeth says
I just took these awesome looking pumpkin cream cheese muffins out of the oven. So easy to make. waiting for them to cool.
YUM!!!
Deborah says
I didn’t have pumpkin so I used 3/4 can of carrots. omg it is good.
Christine Czyryca says
haven’t tasted it yet. looks good but not a 5 star. doesn’t make enough batter and way too much filling left over so these measurements are off for 12 cupcakes.
Carolyn says
Not sure what you did incorrectly but the batter is absolutely sufficient for 12 muffins. This recipe has been made by thousands of people without this issue.
Julie Entrekin says
I just made these and they were DELICIOUS! I’m so thankful for you and others who post wonderful recipes for people like me–not skilled at coming up with my own recipes. Without you and those like you, I would never be able to continue on the keto diet that controls my IBS and has changed my life. Bless you!
Jacqueline D Wright says
These look delicious! Can you use vanilla protein powder without changing the flavor too much?
Carolyn says
Yes, but don’t add the extra vanilla.
Bronwen McKnight says
I made these a while ago and froze half. Just took them out yesterda, had one with coffee this morning. SO DELICIOUS!!! Thank You, Thank You for all you do to help us eat healthy. Off to find a muffin recipe with bacon. I’m sure you have one….
Clare Wallace says
love the muffins, but wish I could share it to the Carb Manager app. W ould make tracking macros so much easier
Stacy says
My ten-year old and I made these today. They were super simple and very tasty. We didn’t have heavy cream, so I just used a little unsweetened almond milk. They still turned out amazing. The muffin is almost the consistency of pumpkin pie, so it’s like having pumpkin pie cheesecake. I was trying to decide what to do with the rest of the can of pumpkin, but now I know thar we’ll have to make more of these to share.
Carolyn says
Great to hear!
Martha Tanner says
Can I substitute honey or maple syrup for Swerve Sweetener? looking forward to making this!
Carolyn says
I am sorry, I don’t use them. But I think you risk throwing off the wet to dry ratio.
Iris says
Hi Carolyn! 🤗
May I used unflavored gelatin instead of whey protein?
Pls, let me know .
Thanks for all your recipes 🥰🥰
Carolyn says
Gelatin is not a good sub for protein powder. It will make the muffins gummy and hard to cook through.
Jeni Kate says
I had some leftover pumpkin puree from making another recipe from All day I dream about food. I decided to make these pumpkin cream cheese muffins and they don’t disappoint! I decided to freeze half the batch so I can have some now and enjoy again at a later date!
Carolyn says
So glad you enjoyed them!
Bronwen McKnight says
Morning Caroline, it’s a drizzly fall day here in Merrickville ( small town on the Rideau Canal outside of Ottawa). Just warmed a Pumpkin Spice Muffin and poured another cup of coffee while browsing through your Soups and Stews Recipes book, figuring out what to make for dinner! Thank you for all you do!
Carolyn says
Thank you! Enjoy your day.
COLLEEN PRUSHA says
Another winner, Carolyn! (I have yet to find any of your recipes less than 5*) These made up easy. I chose to swirl the cream cheese middle with the top scoop of batter and they were like velvet in my mouth with that rich, sweet pumpkin spice flavor. I have silicone baking cups and they are 3 different shapes so I could not fit them in a muffin tin. I set them on a baking sheet and they took 27 minutes to look set on top with the edges just turning brown. They probably could have used another minute. The mix filled my cups to the very top and a couple of them ran over but even those bits were delicious. We each ate one and froze the rest. These are definitely dessert quality and will be on the weekly rotation.
Lucy Provost says
Nicely sized flavor-packed portions of spicy and creamy goodness. I froze a few of them and they thawed out nicely, although the crumb consistency wasn’t quite as nice as when fresh. Best way to eat them (besides fresh out of the oven!) is to warm them up for 20 seconds in the microwave. Yum!
Patty Spiro says
A nice variety to add to breakfast.
Too tender to eat without a fork – but that was fine.
I put some chopped walnuts on top and a sprinkle of extra pumpkin spice.
Great flavor. Having the leftovers today 🙂
Sherry says
These tasted better with each day that they were stored in the fridge. Made them with the cream cheese and without it. So good! Thank you for your hard work and dedication.