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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Carolyn – do you have to use the protein powder in these? I do not buy protein powder because they all taste so nasty. Any substitute or can it be omitted? 1/4 c might be too much to omit.
You don’t but… it rises better with it. That said, when you use unflavored protein powder in a recipe like this, you totally won’t taste it at all.
These muffins were a huge hit at our house!! My husband ate 4 of them and said they were the best muffins I ever made (this from a guy who doesn’t bother if it’s not chocolate!!) My son said they tasted like a cupcake with the frosting inside. Not a single one was left. Thanks for the great recipes. It makes our lo-carb life so much easier.
Wow, that’s wonderful to hear!
Carolyn, thank you so much for posting a video! Usually I skip videos, but was glad for one this time. I made these in muffin top pans (sans cream cheese) and had difficulty determining how many tops to make, because guessing how much a batter will rise while baking is always a crapshoot for me. Seeing how full your muffin cups were was very helpful. My batch is still in the oven, but the batter was delectable!
My tops are out of the oven, and they are fantastic! I’m going to make the cream cheese mixture and use it as a spread for them, but they’re great unaccompanied. Thank you, Carolyn. I was able to make 16 3″ muffin tops, in case anyone wonders about doing the same.
Glad you like it!
Has anyone tried these with SF chic chips? I love pumpkin bread/muffins with chocolate chips!
*choc chips
Can these be made without the whey protein powder?
Yes but they may not rise as well.
I just made the muffins today without the whey powder, I just substituted it with more almond flour, and you’re right they didn’t rise much, but I still thought they were great! I used to love these muffins at Starbucks before I found out I was gluten intolerant, and before I began to follow a low carb lifestyle so it’s great to have a substitute! Thank you 🙂
Glad to hear it!
I could not go a day without using one of your recipes. Thanks for picking a great one today. LOVE pumpkin this time of year!
This recipe is incredible! My husband, who has had a life-long hatred of pumpkin, loves these muffins. He’s a good sport and has always tasted all of the pumpkin recipes I have made. This is the first one he has ever liked. My daughter and I both love pumpkin and, of course, we love these muffins. I’m planning to make these at Thanksgiving when my grown kids will be here. But I will be making them a lot before Thanksgiving. I have cream cheese softening on the counter so I can make another batch today. Thank you so much for all the wonderful recipes. I’ve made and loved many of them. I’m anxiously waiting the upcoming release of your cookbook.
Oh Carolyn, these look fantastic. Watching the video, I wish I had these made for breakfast this morning! So glad it’s pumpkin season!
Yum! Can’t wait to try these. Think almond milk can be used in place of the heavy cream?
For the filling? Yes but probably half the amount as it may make it too thin.
Made these today. Wonderfully delicious! Thank you for another winner!
Glad you liked them!
What type of liners do you use(I use parchment one now but they pull away from everything and sweat as well) and also what kind of hand mixer do you have? I need a new one that does not splatter stuff everywhere:)
I use parchment too, that’s what you see here. I use the ones from Paper Chef. My hand mixer is just a cheapie Proctor Silex one.
Carolyn I just made these muffins today and they are delicious! Thanks for sharing your recipes with us! I love every one of your recipes I’ve tried so far. Looking forward to trying more! Thank you.
Thanks, Louise.
Carolyn, I have been making these for a couple years now, even in the “off” season! I have taught my 12yo daughter to make them and she does a fine job. We always double them as they go so quickly! I leave the cream cheese out of some for my hubby as he is not a fan, but loves the pumpkin.I also use walnuts on top as I rarely have enough pepitas around. I think we need a batch today!
Ha I left the cream cheese center out of 6 of these and put chocolate chips in for my kids. They loved them that way!
Ok, yum!!!! I think my favorite thing about all of the recipes of yours that I’ve tried is that they’re not super sweet. I love that these are subtly sweet, moist and really delicious! I did not do the topping only because I didn’t feel like going to the store and I needed a good, high-protein snack for the kids before volleyball. These really hit the spot! Both girls won their volleyball games… Coincidence? I think not!
Haha, yay for the volleyball games. I just updated this recipe RIGHT NOW, as a matter of fact. I skipped the topping and simplified the recipe a bit, so I hope you will come back and check it out!
can Neufchatel cheese be used instead of cream cheese?
Probably.
I tried to check through all previous questions, but this is a popular recipe!!! I’m wondering what is the benefit of allowing the pumpkin to drain on paper towels?? I’ve never seen that before. These alternative flours usually make baked goods so dry anyway, it seems counterintuitive????
Almond flour is anything BUT dry, as it has a great deal of fat in it, and baked goods made with it can be overly moist. I think you are thinking of other GF flours like rice flour. So drying the pumpkin out a little can really help when working with almond flour..