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.
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Can anything else be used as a substitute for the whey protein powder?
Only another protein powder. And not collagen protein, it makes things gummy and hard to cook through.
How much would it change the carb count if I used the streusel topping from your Keto Pumpkin Crumb Cake recipe? I think that would put it over the top amazing as most of the pumpkin muffins I eat have the streusel topping.
I am honestly not sure, you will need to run those numbers yourself. I don’t have that offhand. Lovely idea, though!
Can I sub in whipping cream for almond milk?
No it needs to be thinner. Try half cream half water.
This recipe turned out exactly as promised! They were soft and delicious. Thank you!
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! ????????????????????
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.
Lol. Obviously I let it cook but I didn’t let one cool before trying it.
Hah. Got it! 😉
Hi, could I use xanthan gum instead of the protein powder?
Thank you.
No, they don’t work at all the same way.
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.
Can I substitute a plant based protein powder instead of whey?
That should be fine. The only one that really doesn’t work is collagen protein.
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!
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.
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!!
Thank you…. By the way… good thing about hubby is now the only way to go is UP!
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.
Can’t see why not!
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.
Thanks so much, Dawn!
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!
Can you make this into loaf instead of muffins?
I would imagine so but it will take longer to cook.
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.