Keto Pumpkin Muffins with Cream Cheese Swirl

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This Low Carb Keto Pumpkin Muffins with Cream Cheese Filling Recipe made with coconut flour is moist, easy to make, and full of incredible pumpkin flavor. Pumpkin spice season hits, and this is a must in your recipe list!


keto pumpkin cream cheese muffins with the muffin liner opened up and a bite taken out of muffin


Keto Pumpkin Muffins with Cream Cheese Filling

When I posted my Keto Pumpkin Bread, I had no idea how popular it would be. I knew my family loved it, but everyone has different tastes. I typically hold my breath in expectation when I first post a new recipe until I hear feedback from those who have tried it. Thankfully, it was a hit. So much so that I decided to make some modifications to the original recipe and make a low-carb pumpkin muffin with a delicious cream cheese swirl. I knew after taking the first bite of the combination of moist pumpkin bread with a sweet cream cheese filling I had hit the jackpot of all things pumpkin.

Recipes like this that I have adapted to Keto/low carb are a fantastic replacement. However, they will never taste just like their counterpart full of gluten-filled white fluffy flour and regular sugar. Having the appropriate expectation will keep disappointment at bay. These are a really good alternative and a welcome breakfast or a keto dessert.

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You are going to love these simple and delicious Keto Pumpkin Muffins with a cream cheese filling. For more recipes like these, don’t miss my Easy Keto/Low Carb Recipe Facebook Page on Facebook, where I post all my new recipes and follow me on Pinterest here.

If you are just getting started following a keto diet and would like more information, there are tons of fantastic resources. Amazon has several great books you may want to check out here. I also posted a great list of Best Keto Resources for Newbies that are very helpful.

Is Pumpkin Keto Friendly?

In moderation, pumpkin is keto-friendly. It is best enjoyed in recipes such as these Keto Pumpkin Muffins with cream cheese as the net carbs are spread over many servings.

What is Pumpkin Puree?

Pumpkin Puree is not the same as pumpkin pie filling. Pumpkin puree doesn’t contain any sugar or spices. You may find it labeled 100% pumpkin or canned pumpkin. Simply put, it is just cooked and mashed pumpkin. If you prefer to make homemade pumpkin puree, the measurement would be the same.

ingredients for gluten free muffins

Even if you aren’t an experienced baker, these quick and easy keto pumpkin muffins with coconut flour are dangerously simple to make. With just a few steps, you combine the wet ingredients first then the dry ingredients next. The batter will be extremely thick. That is normal when using coconut flour since it is so absorbent.

spooning batter for keto pumpkin muffins cream cheese filling in the muffin pan

As I had mentioned above, I prefer using parchment paper liners for the muffin cups so that the batter doesn’t stick. Once these delicious gluten-free pumpkin muffins are done, they pop right out of the muffin tin, and the liners peel off easily.

cream cheese filling for keto pumpkin muffins

The cream cheese filling is an incredible addition to this keto pumpkin muffin recipe. Adding a little vanilla extract gives it the perfect flavor. You’ll love the combination of pumpkin spice and cream cheese filling when you take a bite into a hot keto pumpkin muffin straight out of the oven.

Pumpkin Keto muffin with cream cheese filling before baking

Spoon the cream cheese filling mixture in the center of the muffin batter, then use a knife or toothpick to swirl the cream cheese into the batter a bit.

Tips to Making Low Carb Pumpkin Muffins:

  • Don’t be afraid of the spices. Pumpkin Pie spice is an incredibly delicious seasoning mix that is full of mouth-watering flavor. If you can’t find pumpkin pie spice at your local grocery store, you can make it homemade. You can find many options for making homemade pumpkin spice on Pinterest.
  • This sugar-free recipe makes 18 regular-sized keto pumpkin muffins. Silicone muffin pan or parchment paper liners are necessary as Keto breads tend to stick to the pan. I prefer parchment paper muffin liners to prevent the muffins from being too “wet” on the bottom since sometimes silicone pans don’t bake evenly.
  • Keto Pumpkin Muffins with coconut flour are moist and delicious, but if you prefer almond flour, it is a suitable conversion at a 1:4 ratio (1/4 cup coconut flour equals 1 cup almond flour).
  • Lakanto Monkfruit sweetener is my favorite; however, you can substitute the Monkfruit powdered with Swerve Confectioners.

Can I Make These Keto Pumpkin Muffin Recipe Dairy Free?

I am personally not dairy-free, so I have not tried these substitutions myself. As someone who understands the seriousness of food allergies, I suggest double-checking the ingredients yourself to make sure I did not miss anything.

  1. Substitute Full Fat Coconut Milk for Heavy Whipping Cream
  2. Substitute coconut oil for butter
  3. Make homemade dairy-free cream cheese to use in the place of regular cream cheese.

low carb muffins out of the oven in muffin tin

How to Store Low Carb Pumpkin Muffins

These Pumpkin Keto Muffins are best kept refrigerated in an airtight container for a week or the freezer in a freezer-safe container or freezer zip lock bag for 4-6 months.

keto pumpkin muffins with a bite taken out

Yum! These delicious Keto Pumpkin Muffins taste amazing and make a delicious breakfast with a cup of coffee or an after-dinner keto treat.

Variations to This Recipe:

  • Add Crushed pecans to the top before baking
  • Throw in a few sugar-free Lily’s Chocolate Chips
  • Make Mini Muffins instead of regular-sized for a delicious bite-sized treat.

More Keto Pumpkin Recipes:

low carb pumpkin cream cheese muffin with a bite taken out of it
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4.62 from 213 votes

Keto Pumpkin Muffins with a Cream Cheese Swirl {keto friendly/low carb}

These Keto Pumpkin Muffins with a Cream Cheese Swirl Recipe are easy to make, delicious, and full of incredible pumpkin spice flavor, making them the perfect breakfast or dessert.
Prep Time10 mins
Cook Time20 mins
Total Time30 mins
Course: Breakfast, Dessert
Cuisine: American
Keyword: Keto Pumpkin Muffins, Low Carb Pumpkin Muffins
Servings: 18
Calories: 121kcal
Author: Kasey Trenum


For the Muffins:

For the Filling:

  • 3 oz cream cheese room temperature
  • 1 tablespoon heavy whipping cream
  • 1 1/2 tablespoon Lakanto Monkfruit Powdered
  • 1/2 teaspoon vanilla extract


  • Melt coconut oil and butter. ( I have started using liquid coconut oil for baking). 
  • Beat eggs, Lakanto Monkfruit Powdered, pumpkin puree, vanilla, and pumpkin pie spice until combined.
  • Add coconut oil and butter to the mixture and mix well. 
  • Add coconut flour, salt, and baking powder to other ingredients, then mix thoroughly and set aside. 
  • In a small bowl, combine the ingredients for the filling and stir until combined.
  • Fill greased muffin tins with batter. (I would suggest using a silicone muffin pan or parchment paper muffin liners as keto baking items tend to stick.)
  • Spoon approx 1/2 teaspoon cream cheese filling mixture on top. With a toothpick, swirl the cream cheese mixture into the batter.
  • Bake in a 350-degree oven for 18-22 minutes or until a knife inserted comes out clean. My muffins were perfect at 20 minutes, but every oven cooks differently. 



The sugar alcohols in the Lakanto Monkfruit are not included in the nutritional information since most subtract to get net carbs. 
The nutritional info is based on the ingredients I used in my kitchen. I would encourage you to calculate your own based on the ingredients you use. 


Serving: 1muffin | Calories: 121kcal | Carbohydrates: 3g | Protein: 2g | Fat: 10g | Fiber: 1g
Tried this recipe?Mention @kaseytrenumblogger or tag #kaseytrenumblogger!



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  1. 5 stars
    I’m in heaven … the smell of these is one more reason to transition our house to being passive (could it please trap in the smell of these muffins forever?!). I hand ground the pumpkin spice and added allspice and cardamom. Thank you for this incredible recipe 😍

  2. 5 stars
    Made these with my daughter. They are moist and delicious . Very easy to make. Like dessert when you heat them. My oven took 25 – 30 mins to bake them but you have to keep checking them.

  3. 5 stars
    A W E S O M E. WOW. If someone had given me one of these even before I started keto, I would have been just as impressed. SO moist and delicious (+ made our house smell wonderful while baking). Thank you!!

    1. I don’t know. Applesauce isn’t considered keto-friendly so I haven’t tested the recipe with it to know if it would work or not.

    1. The recipe calls for one cup of pumpkin puree so it really doesn’t matter what size can you buy as long as it yields one cup.

  4. Great recipe! I love all things pumpkin and this did not disappoint. Will definitely be making these again and may even cut back on the sugar slightly so they are not as sweet.

    1. Awesome. So glad you loved it. I always reduce the amount of sweeteners for myself, but everyone is different. If you feel you need to cut back I would def do so next time. I’d really appreciate you rating the recipe on the recipe card with the star rating.

  5. 5 stars
    The family loved these muffins!!
    How can I figure my the nutrition values as I had different brand ingredients as you used. All low carb just different brands?
    What brand of pumpkin did you use?

    1. You could use just about any keto app. I have used different brands of pumpkin puree. It is all pumpkin puree which is nothing but pumpkin with no other ingredients.

  6. 5 stars
    It’s nice to have a delicious desert when dieting. These muffins are moist and tasty….my husband loves them too.

    1. I’m sure you can, but I haven’t tested it as a cake. I’d prob start at 350 then check it often, but that is just a guess.

  7. 5 stars
    These are delicious. I made them exactly as directed. The recipe made 18 muffins. I may decrease the sweetener next time, only because it’s expensive.

    1. Fantastic! So glad you loved them. The longer I eat low carb, I have found I can use less sweetener.

  8. Hi!
    What do you mean by vanilla? I know you mentioned vanilla extract but then I’m seeking just vanilla as well.


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