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.
Cheryl says
These are now considered a family favorite. We like the pumpkin taste to be bold. So, I use 4 tsp of pumpkin spice. They freeze great too! ????????????????????
Marsha says
I just made these tonight and they are yummy!! My house smells so good and I didn’t wait for one to cook completely before trying it. I’ll be making more this week and freezing them since I have pumpkin left over. Thank you for another great recipe.
Marsha says
Lol. Obviously I let it cook but I didn’t let one cool before trying it.
Carolyn says
Hah. Got it! 😉
Carmen says
Hi, could I use xanthan gum instead of the protein powder?
Thank you.
Carolyn says
No, they don’t work at all the same way.
Linda Forslund says
Hi, I have a suggestion, it would be great if you would put a note on your recipes if you can freeze them or not, it’s just my daughter and myself and sometimes we can’t eat fast enough. Love all your recipes, I personally think you are a genius. Thanks for all the great recipes.
Kelly says
Can I substitute a plant based protein powder instead of whey?
Carolyn says
That should be fine. The only one that really doesn’t work is collagen protein.
Jamie says
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!
Gabi says
These are just perfect for fall! I can confidently say that every part of your recipes is amazing…especially the finished product! I follow your ingredients entirely and never feel like I need to modify something…even the baking time and quantity is spot on. Thank you again for your wonderful work! The only downside to this recipe is I only had 12 muffins lol.
Sunne Allen says
I made these but didn’t have enough batter to cover 2 of them. For me it requires more batter but they are so delicious!!
Valerie Roman says
Thank you…. By the way… good thing about hubby is now the only way to go is UP!
Dawnj says
Hello Carolyn,
Since, with your blessing, I doubled the lemon (cream cheese) muffin recipe and made an 8 inch bundt pan cake that was incredible, may I also do the same with this pumpkin cream cheese muffin recipe? And if so, would you double the cream cheese filling as well or would that be too much cream cheese filling? I would be ever so grateful for your expertise. Thank you.
Carolyn says
Can’t see why not!
Dawnj says
Thank you, Carolyn, for answering my recipe question so quick! I will make the bundt cake version today. I love baking and lately, a comforting diversion. Thinking of you and your loved ones.
Carolyn says
Thanks so much, Dawn!
Dawnj says
Your pumpkin recipe for this cake is the BEST I have ever tasted. Could not believe it. Putting the cream cheese in a “tunnel” turned out fabulous. My husband loved this and said it tasted exactly like pumpkin pie in cake form. Thank you for your recipes can tireless guidance!
Trish says
Can you make this into loaf instead of muffins?
Carolyn says
I would imagine so but it will take longer to cook.
JL says
It’s been a while since I made these. Why, oh why? They are fabulous. I’m making another batch right now. Thanks so much for this great recipe.
Kathy says
These muffins are the VERY BEST thing I’ve made using Keto ingredients! Thanks!
Pattey says
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!!!
Patti says
Would love to make these!! Are they “regular” size muffins or mini’s?
Carolyn says
Standard muffin size.
Carol Taylor says
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
Carolyn says
Totally can. Any thin milk will do.
Karen Hayes says
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
Summer says
Hello! What can I sub for the whey protein powder? Thanks!
Carolyn says
Egg white protein powder works too.
Alicia C Conrow says
Any substitute for the whey protein? I just looked it up on Amazon and yikes, that’s expensive!
Carolyn says
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.
Denise says
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
Carolyn says
Thanks, Denise!