Pumpkin Spice Keto Muffins Swirled With Cream Cheese

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Pumpkin spiced keto muffins at only 3g net carbs shouldn’t be this addicting. Keto pumpkin muffins are easy to make, share and get your favorite fall flavors during the holidays!

Originally, I didn’t think you wanted cream cheese in your muffins. So, I created my classic recipe here. It was a bit out of date so I revamped things up just for you with the addition of swirling cream cheese into each muffin.

Now, come Thanksgiving season we are looking for recipes all over the place and pumpkin is a huge criteria. The keto desserts are great but to pair with breakfast during the holidays muffins hit the spot. Well, at any point during the year really. You already have what you need so let’s prepare the batter and start baking!

How To Make Keto Pumpkin Muffins

Ingredients Needed

  • Blanched Almond Flour
  • Coconut Flour
  • Keto Sweetener
  • Baking Powder
  • Pumpkin Pie Spice
  • Cream Cheese
  • Pumpkin Puree (not pumpkin pie filling)
  • Egg
  • Butter
  • Vanilla Extract

Baking The Pumpkin Muffins

The cream cheese part is different from the actual muffin itself. Below I will add instructions because it very similar to a keto cream cheese frosting recipe. But the pumpkin portion is super easy. Here are the step by step instructions:

  1. Start by combining all of your dry ingredients.
  2. Add all your wet ingredients next. But, a little trick I learned was to pat the excess water from the canned pumpkin with a towel. This will help big time in keto baking because gluten free and starch free flours don’t absorb excess water.
  3. Lastly, combine dry and wet ingredients together. You can use a hand mixer or simply fold them in as I do. I sift my almond flour and other dry ingredients. So, that allows me to fold smoothly.
  4. After ingredients are combined I will start to pour in silicone muffin cups or paper liners inside a muffin tin or pan.
  5. Bake for 25-30 minutes or until a toothpick comes out clean.

Helpful Recipe Tips

  • Tips on the cream cheese, on average I use about 1/2 teaspoons to 1 of cream cheese in each muffin. Be sure to swirl the cream cheese as much as possible.
  • You can skip the cream cheese altogether and follow the recipe without that portion.
  • Allow these to cool completely! Almond flour is very fragile when fresh out of the oven and even more with cream cheese swirling through it.
  • Create homemade pumpkin spice. This mix contains cinnamon, ginger, ground cloves and nutmeg. If you need a little help I created one in my keto pumpkin cheesecake recipe.

How To Store

This recipe makes 6 keto muffins. In the situation where there may be leftovers store them in the refrigerator in an airtight container or simple a plastic bag. You can store them in the freezer as well. Simply make the muffins, allow them to cool fully then freeze them in a storage container and thaw them before eating.


maple cream cheese keto pumpkin muffins split in half

Pumpkin Spice Keto Muffins Swirled With Cream Cheese

Pumpkin spiced keto muffins at only 3g net carbs shouldn't be this addicting. Keto pumpkin muffins are easy to make, share and get your favorite fall flavors during the holidays!
3.64 from 19 votes
Prep Time 10 minutes
Cook Time 25 minutes
Total Time 35 minutes
Course Breakfast, Side Dish
Cuisine American
Servings 6 muffins
Calories 171.1 kcal


  • 1 cup blanched almond flour
  • 2 tablespoon coconut flour
  • 1/4 cup granulated sweetener
  • 2 teaspoon pumpkin spice
  • 1/2 teaspoon baking powder
  • 1/4 teaspoon salt
  • 2 large eggs
  • 4 tablespoon unsalted butter
  • 2 tablespoon canned pumpkin (optional but recommended)

cream cheese mixture

  • 2 ounces cream cheese
  • 1 tablespoon sour cream
  • 2 tablespoon sweetener
  • 1/2 teaspoon vanilla extract


  • Preheat the oven to 325-330ºF
  • Mix almond flour, coconut flour, sweetener, pumpkin spice, baking powder and salt together for your dry ingredients
  • Note: Before adding canned pumpkin into batter be sure to pat excess water off with a paper towel.
  • For your wet, melted butter, eggs, canned pumpkin, and liquid stevia or monk fruit. Mix those together.
  • Combine dry and wet, cream cheese instructions below.
  • Take 1/2 TB of the pumpkin muffin batter and line the bottoms of your muffins liners. Then take 1 tsp of your cream cheese and place on the top of each. Next, on top of that add 1 TB of pumpkin muffin batter then 1/2-1 tsp of cream cheese batter on top of that. Then using a toothpick give the top portion a swirl.
  • If you notice you are alternating the two creating layers. Place in preheated oven for 25-30 minutes checking at the 20 minute mark. Muffins should have risen and toothpick should come out clean.

Cream cheese batter

  • Cream room temperature cream cheese with a hand mixer
  • add in sour cream, vanilla extract and sweetener then cream everything together



Nutrition Facts
Pumpkin Spice Keto Muffins Swirled With Cream Cheese
Amount Per Serving (1 muffin)
Calories 171.1 Calories from Fat 140
% Daily Value*
Fat 15.6g24%
Saturated Fat 5.8g36%
Trans Fat 0.2g
Cholesterol 84.4mg28%
Sodium 47.8mg2%
Carbohydrates 4.4g1%
Fiber 2g8%
Sugar 1.5g2%
Protein 5.6g11%
* Percent Daily Values are based on a 2000 calorie diet.
Keyword keto pumpkin muffins
Tried this recipe?Leave a rating and comment, thank you

11 thoughts on “Pumpkin Spice Keto Muffins Swirled With Cream Cheese”

  1. 4 stars
    I’m confused, in the video you show adding an egg. To the cream cheese mixture, but the recipe doesn’t. Also the videos stops at that part ……. You don’t show how to layer it all.

  2. I am aware of the differences and I apologize for any confusion. Over time with experience I go back and recreate recipes to give you the best recipe possible. I have to update the video to match now and make the instructions clear on what to do for you. My apologies, the holiday season is approaching and I plan to have that out by September.

  3. Wow can’t wait to try your recipe! Glad I found your site! Just a little surprised at the small amount of pumpkin called for in this pumpkin muffin recipe. (Only 3 Tbsp vs the cup normally called for). Was that a typo or is there a specific reason you use such a small amount?

  4. No that isn’t a typo. Pumpkin contains a bunch of water. Granted you can drain some off but when you don’t have gluten or something as absorbent as flour things will turn from moist to mushy very quickly. I like to make sure the pumpkin flavor is still there without losing that great texture.

  5. How can I find your original pumpkin muffins recipe? The link you provided takes me back to the new one. Thanks

  6. Hi, which muffin recipe was it? Was it the plain pumpkin muffins or the old version of this one?

  7. It says maple cream cheese mixture but there’s nothing maple in the recipe. Am I missing something?

  8. Darius Pittman

    Correct, the recipe was changed but I left the option to use maple extract instead of the vanilla because people did enjoy the original recipe. I apologize for the confusion.

  9. Great muffins if you can get through the very confusing directions. Recipe needs one direction with variations as option.

  10. I am glad you enjoyed them but what was confusing? This way I could clear it up for anyone that may run into the same issue, thanks in advance.

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