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.
Dom Serrone says
Exceeded my expectations. I even fooled my daughter who normally shuns anything LOW CARB.
Very moist and creamy.
2night I’m going to zap one on the Micr for 20 seconds and then put a bit of Low carb vanilla ice cream on top.
BTW: Thanks for what ever you have done to your website- because now I can directly import your recipes to my Paprika app. I still rather use your cookbooks when home, but many of your online recipes need to be saved to MacBook and iPad so I have them with us when travel.
Thanks for you wonderful WebSite. I’m an identical twin whose brother is a diabetic. So I’m convinced that Low Carb cooking and exercise have kept me healthy. I’m 75+ and my labs are always impeccable.
S Kagan says
I made the original recipe and they came out delicious. They are perfect with a cup of coffee, for breakfast, but also, I had them as dessert after dinner with a cup of tea. Perfect pumpkin taste without over doing it. My only suggestion would be to reduce the sweetener in the muffin by about 1/4 cup, but I like a less sweet muffin.
Rebecca says
I just made these for the first time and gobbled one down as soon as it was cool enough to eat. So moist and delicious! I will definitely be making them again.
Sheri says
These were so dang good!!! I ate all 12 over three days lol. You are my go-to for ALL keto desserts! Thank you, Carolyn!
Dana says
I made these muffins this morning! I omitted the cream cheese filling and added Lily’s dark chocolate chips instead. I ate one and it was just delicious! This will definitely be my go-to keto pumpkin muffin recipe!
Gayle DiGiovanni says
If you are looking for a way to welcome Fall with the flavors of pumpkin and cinnamon mixed into a moist delicious keto muffin – this recipe is for you! The cream cheese filling was a bonus! As usual the instructions were flawless. I made the cream cheese in the middle version and sprinkled some cinnamon sugar on top that I had left over from the Keto Pumpkin Donuts- also a winner!
Darcy says
These muffins are nothing short of amazing! Everyone in my family absolutely loves them and no complaints from anyone about them being low-carb and sugar free! These muffins are moist, tender and satisfies any sweet-tooth. They taste like pumpkin pie with sweet cream cheese filling. Thank you for your amazing recipes!
Linda says
I definitely don’t need a contest to encourage me to make these muffins. They are my favorite sweet recipe of yours by FAR. I’ve made them many times and not just in the fall. I love nothing more than to sit on my porch with one of these muffins and my morning coffee. It makes me gloriously happy. So now that I’ve made the muffins again you can probably guess that I’m once again gloriously happy.
Shelly says
These are really delicious, though mine took closer to 35 minutes to cook. I especially enjoyed the cream cheese filling, and can see repurposing that in other baking projects.
Nancy Lura says
Healthy delicious fall muffins! I made these and they were devoured by my family, I have to make more!! 🤣✌🏼
Mariea says
These are delicious and a favorite of mine. They are very easy, too, which is a HUGE plus. Thank you!
Janet Worley says
Made these pumpkin muffins tonight and my husband and I could not wait until tomorrow morning. He put a little Keto whipped cream on top. As he said, these muffins are keepers. They were moist and delicious. I will make these all fall and winter! Thanks for a go to muffins recipe! Yum!
Alice says
I just made these, I use half almond flour & half peanut flour.
They were still a bit warm, very good. I put the rest in frig.
I will definitely make these again.
Sara Karlich says
These are simply the best. Great flavor and texture.
Sylvia says
This a fantastic recipe (as usual) I absolutely love these muffins . Thank you for all the wonder Recipes.
Ilana Joffe says
This is my all-time favorite muffin. Like most of Carolyn’s recipes, this is easy to make and delicious to eat!
Dawn Diamond says
I love these muffins, they freeze quite nicely as well, yes I actually managed to keep some to freeze. I have to really discipline myself not to binge eat them. Whipped up some cream to dab on top. Pure heaven.
Thank you Carolyn
Nicole Schroedermeier says
Feeling like fall today and these are always top of my pumpkin list! My whole family loves these. I added some Lilys salted caramel chocolate chips for a little extra yumminess. (although they need nothing extra)
HR says
My hubby is not a fan of cream cheese but he loves pumpkin anything. Can I just omit the cream cheese or do I need to double the recipe to make up the void?
Carolyn says
Hi, I write about that already in the post! 🙂
Dori Miller says
These looked so good I had to make them today. It was the first time I used egg white protein in my baking. I’m trying to build up my Keto pantry slowly, 1 product at a time. Next is the peanut flour.
These muffins came out perfectly. Texture was spot on, flavor was very good, truly a fall time treat. They looked just like your pictures, score! The ultimate compliment, my husband asked for seconds!! They were not overly sweet, which I liked .50 g of Swerve, I did add 10g allulose, since I have the cold sensation from the Swerve alone. I might up the spices and add a little more Swerve next time. Otherwise, perfect.