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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I made these today, and they are nothing short of amazing! Truly one of the most delicious LC GF treats I’ve ever enjoyed. I skipped the pepitas (didn’t have any). Thanks for sharing.
I use plain pecans. These make wonderful small loaves also
Great idea!!!
Thanks, Pam!
I was wondering how I’d get by without my Starbucks pumpkin muffin! Now I know!!! 🙂 made these tonight! DELICIOUS!!!
Carolyn,
Are whey protein powder and egg white protein powder interchangable in your baking recipes? Thanks in advance, Sandi
Yes, I think they are. I have used egg white powder in a few recipes and had good results.
Thanks for the quick response, Carolyn. I’m going to go make these muffins right now!
I made these yesterday and they are almost gone already! So so so good! I might add in some pumpkin spice or something next time but I’m just starting a low carb diet so I’m probably just still used to super sugary food. These were amazing though.
First time making these last night, they were outstanding! My son, who is a chef, said they were the best low carb version of anything we’ve ever made. Also, my first time working with Swerve, which I think is an outstanding sweetener. I finally located it at our Whole Foods that recently opened, and I used a coffee/spice grinder to powder it for the cream cheese filling. Again, just a really outstanding recipe, thanks so much for sharing!
Wow, that is high praise. So glad your son liked them too!
so impressed caroline!! absolutely delicious and beautiful….. by far my favorite so far! thank you so very much for all you do for all of us!
oops! i’m so sorry for misspelling your name carolyn…. everyone always puts an “h” in mine!!! caroline or carolyn, what your real name should be is wonder woman!!!
It’s okay, so many people call me Caroline, it rarely phases me 😉
These are hands-down the best low carb pumpkin muffins of any low carb cooking site. We’ve tried many recipes and these are fabulous! Thanks very much!
You’re welcome.
I have made several of your wonderful recipes and passed your blog along to my friends. These yummy muffins are my favorite so far followed by the orange cardamom biscotti . It’s nice to be able to enjoy something besides “meat and eggs” with my morning coffee
I agree, it is so nice not to just rely on bacon and eggs in the morning!
I have serious kidney issues and I’m always trying to reduce the protein and phosphorus content of food I eat (in addition to restricting carbs). It makes for a walk through a minefield. I have already had to replace the baking powder (wicked high in phosphorus and pepitas–also very high). What’s left is to ask you about 2 ingredients in this: eggs and whey powder. Egg whites are low in phosph. but the yolks are high. And whey protein is also high. Could the whole eggs be replaced with just the whites? Is there something that can sub for the whey powder? Since I don’t know exactly what its function is, I can’t answer the question for myself. Thank you for all your great recipes. I wish I weren’t so limited in what I can eat.
Hi Marcia…okay, go for 3 egg whites and for the whey powder, you can use either egg white powder (sometimes called meringue powder) or hemp protein (don’t know if that’s lower in phosphorus. For the baking powder, you can sub baking soda and cream of tartar, do you have that?
The whey protein is to replace the gluten. Gluten is a protein so adding protein helps things rise and hold their shape properly!
Thank you. I do have the baking powder sub. Do you think psyllium could sub for whey? I use it in a lot of other low carb baking to hold things together. There is very little info about hemp on the Internet. What I found says that 100grams is the equivalent of 1 whole egg (in phosph), so that’s not too bad. Would it sub 1:1 for whey?
i’ve never used psyllium so I can’t say. But these sink a little in the middle anyway, because of the cream cheese filling. so I say go for it!
Hi Ms Carolyn 🙂 I’ve just started my foray into a gluten free world due to my recently discovered non celiac gluten sensitivities, but I’ve been low carb for many years. Your website has been a godsend. I made these last night and they were fantastic, out of the 16 I ended up with there are 3 left…husband and kids loved them too! For our families tastes I will add a bit more pumpkin next time and some more erythritol in both the cream cheese filling and pumpkin muffins…but this was just a great, great recipe. Thank you for all you do!
Thanks, Megan!
Hi Carolyn. Another great recipe! I left the topping off but that’s okay they are still delicious! I make these for my breakfast. I just pop one in a baggie everyday and take it to work with me. They are super yummy! Thanks.
These were amazing…. and I even messed up the recipe and they still came out great!! I didn’t have enough almond flour and used extra vanilla whey protein… Still wonderful. Thanks for the wonderful recipes!!!
made these today and they are *insanely* good. thank you so much!!!
Glad to hear it!
These muffins are delicious!!!! I didn’t have whey protein powder, but did have hemp protein powder, so I used it. I will most definitely make them again and again!! I refrigerated them after cooking because of the cream cheese – is that necessary?
They are okay on the counter for a day, but after that, definitely in the fridge. Glad you liked them!
This is becoming my most requested cake. I’ve made it as muffins, mini muffins, and recently as small loaf cakes. I put raw pecans on the top instead of the candied pumpkin seeds. MMMMMMMMMMMMMMM
I’ll be sharing on my blog. THANKS
OH MY!!!! Me and my daughter made these last night. Easily the best pumpkin muffin recipe I have made lately. I started my venture of low carb, gluten free, sugar free in march and am so glad I found your site. I have made several of your recipes and am ways happy with the results. Keep up the excellent work.
Thank you, Manda!