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.
Christy says
These were amazing! First “normal” tasting muffin I’ve tried. So, so good for breakfast or dessert. 😊
Kris Baldwin says
Made these last night for the morning. I always get….more cream cheese….so next time I’ll make a small batch extra for the top. Mine took a little longer to bake. I used a little more ginger, as it is our favorite. They came out beautifully. Next time I will put the cream cheese on the top too!
Jennifer says
I made these for me and my family. I doubled the recipe like someone had suggested. My son especially enjoyed them and I would have them with coffee. It was a yummy breakfast and a dessert. Needless to say, they are already gone. I will try bake them again.
Carla Hubbard says
I made a batch to take to work for my breakfast. They are yummy and freeze quite well. I live in a very rural area and all ingredients were readily available.
Jamie Wynn says
I love these!! Instead of the protein mix I substitute it with cocoa powder and it hit the spot on all levels. Nice chocolate with an underlying pumpkin flavour and to top it off a surprise in the middle!! Yum
Pat Jennissen says
These muffins are so rich and delicious, my family goes through a batch very quickly. They are definitely a fall favourite at our gatherings.
DM says
This is an excellent recipe! Loved the cream cheese surprise filling….this was like pumpkin roll in a muffin. I ate two and had to put the rest in the freezer so I wouldn’t eat them. Love getting your emails!
Kathy McBride says
Just made these last night. Great flavor. Very moist with the cream cheese center. Had a little extra so a few got frosted with it.
Kim Harbeck says
These muffins are really good. Moist, and flavorful. Love making them as mini muffins, easy to snack on. Great appetizer for a fall get together.
Susan says
These muffins turned out perfectly, no one is aware they are keto! I made a bit of extra cream cheese filling to do both the fill and swirl technique! I will be definitely making these again.
Debbie Zapolski says
These pumpkin muffins tasted exactly like my non keto pumpkin roll!!!! Super easy to make and these will be a hit for Thanksgiving day! I made extra filling to use as frosting!!
BRENDA D says
These where absolutely delightful!! This batch made me about a dozen muffins and a mini loaf. Even my partner who isn’t a fan of pumpkin loved these. Will have to make again and swirl the cream cheese around for even distribution next time.
Ambre says
I love this recipe, but I like to pipe the cream cheese filling on top. along with a cup of coffee is a great combination.
Jaime says
This was the first of Carolyn’s recipes I ever made way back when. It is a repeat in my household. Even non-keto people ask for the recipe and can scarcely believe it is low-carb. I did learn along the way that traditional paper muffin cups are a bit tricky with this and most keto recipes because they stick. Since switching to parchment or silicone liners, I’m better able to snap up every last crumb of goodness.
Fran says
September Keto Baking Challenge! Keto Pumpkin Muffins
These muffins are delicious! I baked them per the instructions and they came out moist and flavorful. The filling stayed in the middle of the muffins, it too was moist and cheesecake like. These are great any time of day, as part of breakfast or for a snack.
Fall is coming, time for pumpkin muffins!
Marla Weigel says
Love the combination of the pumpkin and the yummy cream cheese filling! The recipe was easy to make and I’m excited to make more of your pumpkin recipes!
Beth says
These muffins are delicious! I will be making them again. My family enjoyed them too.
Kimberly says
Omg, these are so good. I made them today and I’m trying really hard not eat a half a dozen today. My family is saying Keto or not these are good. I may have to make another batch tomorrow. ❤️ 😍
Sue says
Oh these muffins are soooo good, first time making these and I had a duck egg so I used that with a fresh chicken egg….don’t know if that is what made them so fluffy or just the great recipe but I love them!!
Carol Rivers says
I made half a recipe today for the monthly contest, as I only had two people I was cooking for. It was simple, and yummy! I will be making these again.
Carolyn says
Excellent!