Low carb Pumpkin Cream Cheese Muffins. Giving these super popular keto muffins a brand new update, with a how-to video. Move over, Starbucks, there’s a healthier pumpkin muffin in town.

These are the best low carb pumpkin muffins, stuffed with cream cheese just like Starbucks!

It was time to give one of my most popular low carb muffins recipes an update. It’s almost pumpkin season and I am eager to get going on it. Okay, so it’s not yet September but I still feel an early pumpkin recipe is in order. Plus…the kids went back to school today so it’s time for a proper keto fall celebration, wouldn’t you say? And these sugar-free, gluten-free pumpkin muffins are perfect with your morning coffee. Sip and savor the freedom of a child-free house…that’s what I am doing right now!


The only problem with posting such an early pumpkin recipe is actually finding pumpkin! I had a few cans of pumpkin puree in my pantry so I was good there. But…no cute little decorative pumpkins to show in my photos. Or my how-to video. No grocery stores appear to be carrying them just yet. Somehow the shots just look incomplete to my eyes. But if you can, imagine falling leaves and chilly mornings, kids grabbing their bags and heading off to school, and little mini orange gourds in the background of these photos. I may have to make them again, once those mini pumpkins and gourds are available in stores, just so I can get the photos I want!

Low Carb Keto Pumpkin Cream Cheese Muffins

I had such fun making the video for these. And I simplified the recipe too, because I found a few ways to cut out steps and make them even easier. I also cut down the whole recipe so it makes a proper dozen, instead of 15. While sometimes more is good, it’s not always convenient to have to make more than fits in a regular muffin pan!

Gluten-free pumpkin muffins with a sugar-free cream cheese center

The old pumpkin muffin recipe had you draining the pumpkin puree on paper towels. I find you can skip this step altogether as long as your pumpkin puree is thick and isn’t watery. I used Trader Joe’s Organic pumpkin and found I didn’t need to drain it at all. Instead of beating softened butter with the sweetener and eggs, I just stirred in melted butter, which definitely saves time. And I did away with that candied pepitas (pumpkin seeds) because the reality is that these low carb pumpkin muffins are delicious enough without them!

Fall flavors in a low carb muffin! These pumpkin cream cheese muffins are always a hit

Now, don’t be alarmed if your muffins rise beautifully and then sink a bit as they cool. This appears to be the nature of the beast with cream cheese stuffed goodies. They create a little sink hole as the cream cheese expands and then contracts. It doesn’t matter much…these keto muffins taste as delicious as ever. Like fall in muffin form. How can you beat that?


Preparation 20 minutes Cook Time 25 minutesInactive Time: Total Time:Inactive Time: Total Time:Serves 12 muffins     ADJUST SERVINGS

Low carb Pumpkin Cream Cheese Muffins. Move over, Starbucks, there’s a healthier pumpkin muffin in town.



  • 6 oz cream cheese, softened
  • 3 tbsp powdered Swerve Sweetener
  • 1 tbsp heavy cream
  • 1/2 tsp vanilla


  • 2 cups almond flour
  • 1/2 cup Swerve Sweetener
  • 1/4 cup unflavoured whey protein powder
  • 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 eggs
  • 1/2 cup pumpkin puree
  • 1/4 cup butter, melted
  • 1/4 cup unsweetened almond milk
  • 1/2 tsp vanilla extract


  1. For the cream cheese filling, beat cream cheese with powdered sweetener, cream and vanilla extract until smooth. Set aside.
  2. For the muffins, preheat oven to 325F and line a muffin tin with parchment or silicone liners.
  3. In a medium bowl, whisk together the almond flour, sweetener, protein powder, baking powder, pumpkin pie spice, and salt.
  4. Add the eggs, pumpkin puree, melted butter, almond milk, and vanilla extract. Mix until well combined.
  5. Drop a spoonful of batter into the bottom of prepared muffin tins and use a spoon to make a well in the center. Drop a tablespoon of cream cheese filling into the well, then top with more batter to cover the cream cheese mixture
  6. Bake 23 to 25 minutes, or until tops are set and edges are just browned. Let cool in pan 15 minutes before transferring to a wire rack to cool completely.

by Carolyn


Low Carb Pumpkin Cream Cheese Muffins