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.
EH says
I’d love to try these but I don’t use protein powder. Is there anything I can use to substitute the protein for powder? Thank you! I love your recipes!
Carolyn says
Please understand the science behind banking. Gluten is a protein and in its absence, another dry protein (i.e. not more eggs because that throws off the liquid content) helps the baked goods rise properly and hold their shape. You can skip it but your results may suffer.
Diane says
Made them a second time with just a little more pumpkin and cut the baking time to 21 minutes and they came out perfectly! And – full disclosure – this second time I did make them more sweet by adding 3T of Natural Mate Sucralose All Purpose Sweetener and 20 drops of EZ-Sweetz Liquid Sweetener and I used 8 oz of cream cheese for the delightful center filling surprise. They are just divine!! I served the muffins as a perfect Fall dessert – more like a cupcake. Thanks again for all your fabulous recipes!!
Diane Trapp Paulus says
I used Bob’s Red Mill Super-Fine Almond Flour. I have 4 pounds of it so I must use it. I do prefer Honeyville but don’t have time to get it. Should I just use less? Only the muffin part is a bit dry – the cream cheese is delightful!! You’re the expert so I’ll try whatever you think is best. Just trying to figure out if adding more fat would help or use less of the dry ingredient. Appreciate your help and suggestions!!
Carolyn says
No I always use Bob’s so that’s not the issue. I think you just need to bake them less, since mine are never dry.
Diane says
Absolutely fantastic muffins!! Thank you sooooooo much for doing all the hard work for us. I made them exactly as you said. Baked them for 23 minutes. My only question is – my muffins seemed to come out just a little dry – IF you were to make them just a bit more moist – could you suggest what I should do? i.e., add more butter or cook a few minutes less or cut back on the almond flour, cut back on the temp, etc. Just not sure what to do to make them a bit less dry and I’ll do whatever you suggest and let you know the results. Don’t get me wrong – they were fabulous and I LOVE the cream cheese middle – what a super treat! I plan to make another batch tomorrow and another in 3 days for a ladies fellowship, so I’m hoping you’ll read this soon and be able to reply. Really appreciate your talent!!! THANKS MUCH!!
Carolyn says
What almond flour are you using? These are definitely not dry so that might be the issue.
Janet Adey says
Can you put something instead of whey protein in the recipe?
Carolyn says
You can skip it or use a different kind of protein powder. But if you skip it, they will sink more and wont’ hold together as well.
Jessica says
I don’t have protein powder, can I use collagen powder?
Carolyn says
No, collagen makes baked goods like these very gummy.
Kristyn says
You can never go wrong with pumpkin + cream cheese! Thank you!!
heidi says
In the oven right now! Based on the consumption of batter our family already approves! DELICIOUS!
Bree says
These look soooooo good! I can’t believe they are low-carb!!!
Julie says
What a fun and tasty surprise!
Jessica says
These are amazing! Thanks os much for sharing!
Kimberly says
Positively scrumptious, I am so craving these right now!
Rebekah says
Can the whey protein powder be substituted for something else? My stomach doesnt agree with it.
Thanks.
Carolyn says
Egg white protein works well.
Shauna says
These muffins are AMAZING! Huge hit for my family. Thank you!! What is the best way to store them? Also, does the texture of the filling change if you freeze them and then thaw?
Carolyn says
It may change a little but not noticeably.
Belinda T. says
I made these last weekend and took to a friend’s house for girls game night. Everybody loved them, none were doing Keto, except me. Going to make another batch to take on a trip next week. I left out the protein powder, but everything else was the same. Great recipe, I just love fall flavors! Thanks for sharing.
Barbara Moreda says
Has anyone tried freezing these? I am thinking maybe not with the cream cheese filling. I just made some pumpkin soap and only needed 1/2 cup and had a large can. While I might go ahead and make another bath of soap this week with another 1/2 cup, that still leaves a lot.
Carolyn says
They freeze very well actually.
Andrea Shepherd says
Which cookbook are these in?
I bought the one advertised above and it is not included.
I LOVE LOVE LOVE all your recipes. Thank you for going before us.
Carolyn says
Hi Andrea, most of the recipes on this blog are not in a cookbook. Publishers want new recipes, not ones that are already published.
Kimberly Angerer says
Hi I’m so very new to this woe.. like only 5 days in! I’m wondering if the carb count is net carbs or total carbs? I haven’t made this yet and don’t have all the ingredients to calculate.. but it’s on my to do list! I’m on a mission to prove to my very “meat and taters only” family that this woe can still be great! Thank you for all you do!
Carolyn says
Total carb count. Good luck on your keto journey!
Peggy Deichelbohrer says
These muffins are so amazing. Wonderful flavor and texture. I’m bringing them to my daughter’s home for our early Christmas weekend. They don’t eat low carb but they are gluten free. They will love them. Thanks AGAIN Carolyn!
Penny says
Hi Carolyn,
I absolutely love these Pumpkin Cheesecake Muffins. Do you happened to have a good chocolate muffin that would work the same way to stuff that yummy cream cheese in the middle? Thanks so much. Love love love your blog.
Becky says
So good! Thanks for the remake recipe. I think it’s even better than the original! I’ve made these as written, and then with twice the pumpkin, and this last time I added cranberries for pumpkin cranberry muffins! Very versatile recipe. Thanks again! 🙂