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.
Free Bonus: Secrets to Keto Baking!
Sign up for your favorite recipes delivered straight to your inbox plus get our FREE bonus: Secrets to Keto Baking!
These muffins are the VERY BEST thing I’ve made using Keto ingredients! Thanks!
I made these last night and they were absolutely AMAZING!!!! I used coconut milk because that is what I had on nand and they came out great. I enjoy all your recipes and when I am looking for something in particular, I always come to your site first as your recipes always seem to turn out great. Thanks!!!
Would love to make these!! Are they “regular” size muffins or mini’s?
Standard muffin size.
Carolyn,
I use your recipes all all the time and have loved every one of them so much. I thank you for them.
I am curious however, can I replace almond milk with milkadamia? I usually have it on hand and when i have both, it seems like I end up throwing some of each away. Not really sure how long they keep after opening.
Again, Thank you
Totally can. Any thin milk will do.
This is the best keto dessert I’ve made! Everyone loved them. I made no adjustment to the recipe. I did get parchment cupcake liners, which made removing the cupcake effortless. This recipe is a winner, and perfect for this October weather! I’ll be making them frequently for the next couple of months! Almost forgot to mention….the filling was enough for two batches of cupcakes (24). Thank you!!!
~ Karen
Hello! What can I sub for the whey protein powder? Thanks!
Egg white protein powder works too.
Any substitute for the whey protein? I just looked it up on Amazon and yikes, that’s expensive!
No sub, really. In the absence of gluten, which is a protein, another dry protein helps baked goods rise and hold their shape. You can skip it by they may not rise as well.
Carolyn,
I am so glad I found your website. Your recipes look delicious. I also follow you on Facebook. I am going to try the Pumpkin Cream Chesse Muffins.
Thank you so much for sharing your recipes. I am going to buy your Keto Dinner book and Breakfasts. I can’t wait to get them.
Denise
Thanks, Denise!
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!
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.
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!!
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!!
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.
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!!
What almond flour are you using? These are definitely not dry so that might be the issue.
Can you put something instead of whey protein in the recipe?
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.
I don’t have protein powder, can I use collagen powder?
No, collagen makes baked goods like these very gummy.
You can never go wrong with pumpkin + cream cheese! Thank you!!
In the oven right now! Based on the consumption of batter our family already approves! DELICIOUS!