These incredible Keto Pumpkin Cream Cheese Muffins are the sweet and festive treat you need this fall. Each bite gives you an explosion of delicious pumpkin flavors and a cheesecake filling at just 4 net carbs each!

Cream cheese and pumpkins are two of my ultimate favorite treats. So, I was on a mission to create a muffin that combined my two go-to flavors. I will admit when I bit into these muffins for the first time, I couldn’t help but moan.

The muffins themselves are light, fluffy, and moist. Then the combination of pumpkin flavors with the cream cheese is pure heaven. We make them for breakfast, but also for snacks too. I can’t wait for you to sink your teeth into these incredible muffins.


For the Muffins:

  • Butter – Make sure the butter is room temperature, so it blends perfectly.
  • Swerve Granular– These keto pumpkin muffins are versatile and you can easily use erythritol, monk fruit, or any of your favorite keto sweeteners.
  • Eggs – The eggs help bind the ingredients together to give you delicious muffins.
  • Pumpkin puree – Make sure to use pumpkin puree and not pumpkin pie spice.
  • Vanilla extract – The vanilla takes the pumpkin muffins to the next level.
  • Almond flour – Instead of using regular flour, almond flour keeps these easy muffins low carb.
  • Pumpkin pie spice – Using pumpkin pie spice is exactly what is needed to take these muffins from delicious to extraordinary.
  • Baking soda – To get the best rise out of the muffins you need a little bit of baking soda.
  • Pinch of salt – Just a dash of salt will actually bring out the sweetness in the keto muffins.

For the Cream Cheese Filling:

  • Cream cheese – Be sure to let the cream cheese come to room temperature or toss it in the microwave for 20-30 seconds. Don’t let it melt when microwaving it and allow it time to cool down after heating it up.
  • Powdered erythritol – Just a little bit keeps the keto pumpkin muffins sweet and delightful. We find erythritol is the best it’s a super fine powder and has no after taste.
  • Vanilla extract – The vanilla adds to the flavor too.

How To Make Keto Pumpkin Cream Cheese Muffins

These delicious keto pumpkin cream cheese muffins are one of the best things you will taste and they are only 4 net grams of carbs! Let’s get started so you can head in the kitchen to whip up a batch.

Warm the oven to 350 degrees F. and grease a muffin tin or add muffin liners.

Begin preparing the filling by beating the cream cheese, sweetener, and vanilla in a small bowl. Whisk then set aside.

Next, get the muffin batter ready by beating the butter and sweetener in a large bowl. After they are light and fluffy, beat in the eggs, pumpkin puree, and vanilla. Then add in the almond flour, pumpkin spice baking powder, and salt.

Pour the batter into the muffin tin and add 1 tablespoon of the cream cheese filling to each muffin. Use a fork or toothpick to swirl the batter.

Bake the muffins for 25 minutes or until they are done. Enjoy warm or cooled!

Pumpkin Muffin Variations

  • Add a few sugar-free chocolate chips to the batter. I would only add 1/4 cup – 1/2 cup to the batter and gently fold it in.
  • Drizzle the muffins with some low carb caramel sauce.
  • Throw in some of your favorite nuts to the batter to add a little bit of a crunch. Pecans or walnuts are my favorite.

How Do You Store Keto Pumpkin Cream Cheese Muffins?

For best results, allow the muffins time to cool down all the way. Then place them inside of a storage container that’s airtight. Refrigerate for up to 3 days. They can be kept at room temperature but will spoil quicker.

More Favorite Fall Pumpkin Recipes

4.71 from 48 votes

Keto Pumpkin Cream Cheese Muffins {4 Net Carbs each!}

These incredible Keto Pumpkin Cream Cheese Muffins are the sweet and festive treat you need this fall. Each bite gives you an explosion of delicious pumpkin flavors and a cheesecake filling.
Prep5 minutes
Cook20 minutes
Servings 12 servings


  • 1/4 cup butter, at room temperature
  • 3/4 cup Swerve Granular
  • 2 eggs
  • 1 cup pumpkin puree, (make sure it's pure pumpkin-no sure added!)
  • 1 teaspoon vanilla extract
  • 2 cups almond flour
  • 2 teaspoons pumpkin pie spice, (or 1 and 1/4 teaspoons ground cinnamon, 1/2 teaspoon ground ginger, 1/4 teaspoon ground nutmeg)
  • 1 teaspoon baking soda
  • 1/4 teaspoon salt

For the Cream Cheese Filling


  • Preheat oven to 350F. Grease a 12 count muffin pan or line with parchment liners. Set aside.
  • To make the cream cheese filling:  In a small bowl, beat the cream cheese, erythritol, and vanilla with a small whisk or fork. Set aside.
  • To make muffin batter: In a large bowl, beat the butter and sweetener until light and fluffy. Gradually beat in the eggs, pumpkin puree, and vanilla extract. Whisk in the almond flour, pumpkin spice, baking soda, and pinch of salt and fully incorporated.
  • Divide batter into prepared muffin pan. Spoon about 1 tablespoon of the prepared cream cheese mixture onto each muffin and swirl with a toothpick or fork.
  • Bake for 25 minutes or until cooked through.


Serving: 1muffin, Calories: 208kcal, Carbohydrates: 7g, Protein: 6g, Fat: 19g, Saturated Fat: 6g, Cholesterol: 53mg, Sodium: 231mg, Potassium: 72mg, Fiber: 3g, Sugar: 2g, Vitamin A: 3526IU, Vitamin C: 1mg, Calcium: 66mg, Iron: 1mg

Nutrition information is automatically calculated, so should only be used as an approximation.

Additional Info

Course: Breakfast
Cuisine: American
Keyword: easy, keto, low-carb, lowcarb, muffins
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  1. I used less monkfruit 1/2 C instead of 3/4 and less almond flour 1.5 instead of 2 cups. Used 1.5 C of Pumpkin. Did start to brown too much on top so took them out. Extremely moist. Sis and hubby loved them. Will make again.

    1. I’m so glad you enjoyed it!! Thanks for reporting back!

  2. These were delicious without any changes to the recipe. It’s Halloween so with a little decoration, they really fit in. Incidentally, my neighbors are vegetarians – do these muffins quality as vegetarian … it seems so.

  3. I found the batter rather dry and chunky. Hard to get into muffin tins and even harder to toothpick swirl the cream cheese in. Did I do something wrong? I am still waiting for them to come out of oven

    1. I made these and they are pretty good BUT the total carbs are 18 per muffin. In your ingredients erythritol is list as only 8 carbs. My erythritol is Swerve and for 3/4 cup it has 108 carbs. Not sure why the difference but Swerve on the bag is 3g total carbs per tsp. Too many carbs for me. I will try tweaking this recipe as it is very good for snacking.

  4. Ahhhh. I can hardly taste any pumpkin in these muffins, the almond flour is pretty strong in the recipe. Not sure to why that was since I followed as directed. As for cooking, I did as instructed and the tops Started to burn more and the center wasn’t fully cook. Like another commenter, same happen here. I wish I put the cream cheese frosting after the muffins were done. Frosting honestly didn’t taste yummy when it was cooked and a bit burnt on top. ;(

  5. Really loved the flavor of these. I had problems getting them baked. 1 they stuck terribly to the oiled muffin tin. Guess I should have used the paper liners. 2 Baked for 25 minutes. Tops were firm and very brown and inside was still doughy. Left in for 15 more minutes, ended up with black tops. Any suggestions? Did I use too much cream cheese filling? Should I cover with foil? Again, loved the taste! Thanks.

  6. These muffins were awesome! I have made them 3 times now. The cream cheese and pumpkin make them so moist and delicious. I did cut back on the sugar a little and they were still plenty sweet for me.

  7. Just made these. Eliminated all artificial sweetener because it leaves me with an after taste. Added 2 teaspoons of baking powder. Increased pumpkin to 1.5 cups. Tasty!

  8. soooo good! I changed the sugars to Allulose and it was PERFECT! Just the thing I needed to treat myself. All 3 of my picky young kids ate two each without a complaint other then I wouldn’t allow them another, lol.

  9. Since beginning our keto journey we have made these a staple!

  10. I made these yesterday for my Birthday breakfast. Easy recipe to and quick to make. I got exactly 12 from my batter. Exactly what I was looking for in low carb and high on taste. I did use a bit less sweetener and they came out so tasty. Thank you for sharing this recipe.