Keto Pumpkin Muffins with Cream Cheese Swirl

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Indulge in the comforting flavors of fall with our moist and fluffy keto pumpkin muffins with a cream cheese swirl! Bursting with rich pumpkin spice flavor, they are baked to perfection using pumpkin puree and coconut flour, making them a perfect low-carb breakfast, dessert, or snack. These low-carb muffins are perfect for a keto diet or anyone looking for a healthier alternative to traditional pumpkin muffins.

close up shot of a pumpkin muffin with a cheesecake filling with a bite taken out of it and the muffin paper opened up

Who doesn’t love indulging in warm, freshly baked treats during the fall season? If you’re on a keto diet, you may be missing out on some of your favorite baked goods. But with keto pumpkin muffins, you don’t have to sacrifice flavor for your diet.

Thanks to the pumpkin puree and coconut flour, these muffins are incredibly moist and fluffy. They’re also low-carb, so they make a great keto breakfast or snack option. But don’t let the healthy ingredients fool you – these muffins are still a delicious treat that can satisfy your sweet tooth. The warm spices like cinnamon and nutmeg give them a cozy fall flavor that’s perfect for dessert.

Here’s why you’ll love this recipe:

✔️ Each muffin has only 2 grams of net carbs, making them an excellent option for those on a keto diet.
✔️ The combination of pumpkin puree and almond flour gives these muffins a tender crumb that’s hard to resist.
✔️ This recipe comes together quickly and easily, so you can have fresh muffins in no time.
✔️ These muffins can be enjoyed for breakfast, as a snack, or as a dessert. They’re also great for meal prep and can be frozen for later.

Benefits of Choosing Keto-Friendly Recipes

Keto diets offer many benefits, such as weight loss and mental clarity. Keto-friendly recipes allow you to enjoy your favorite flavors without sacrificing your health goals. Our keto pumpkin muffin recipe is a perfect example of a delicious and nutritious treat that fits within the keto framework.

The Role of Pumpkin in Keto Baking

Pumpkin isn’t just delicious – it adds tons of flavor and moisture to your baked treats. And guess what? It’s pretty low in carbs, perfect for keto-baking. You can get creative and use pumpkin in all sorts of yummy keto recipes like muffins, breads, and cakes.

Is Pumpkin Keto Friendly?

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

Ingredients for Keto-Friendly Pumpkin Muffins

Eggs –act as a binding agent, holding all the ingredients together, contributing to the muffins’ fluffiness.
Coconut Oil – The melted coconut oil adds moisture to the batter, producing soft and tender muffins.
Butter – introduces a rich buttery flavor to the muffins, enhancing their overall taste and texture.
Pumpkin Puree – This ingredient is the heart of the recipe, bringing in the classic pumpkin flavor and moisture that’s essential for that perfect muffin crumb.
Pumpkin Pie Spice – This spice blend is responsible for the warm and comforting pumpkin spice flavor that makes these muffins quintessentially fall.
Wholesome Yum Monkfruit Allulouse Blend Sweetener – adds sweetness without the sugar, making the muffins low-carb and keto-friendly.
Vanilla – adds sweetness and depth to the muffin’s flavor profile.
Coconut Flour – is the gluten-free and low-carb flour alternative that gives structure to the muffins, soaking up moisture and lending a subtle coconut undertone.
Salt -This small amount of salt heightens the flavors of the muffins, balancing the sweetness and enhancing other seasonings.
Baking Powder –  is the leavening agent that causes the muffins to rise, giving them a light and airy texture.

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. The measurement will be the same if you prefer to make homemade pumpkin puree.

Ingredients for gluten-free pumpkin muffins in a clear bowl with pumpkin puree at the bottom and coconut flour and keto-friendly sweetener on top. Cinnamon sticks in the background on a plain kitchen towel

How to Make Keto Muffins with Cream Cheese Filling

Step 1: Preheat your oven to 350°F and prepare your muffin pan by greasing it or using muffin liners. Melt the butter and coconut oil (you can also use liquid coconut oil).

Step 2: Mix all your wet ingredients and the pumpkin pie spice in a large bowl. Make sure that the butter and coconut oil aren’t too warm from melting.

Step 3: Add the dry ingredients and mix everything.

spooning batter for low-carbumpkin muffins made with coconut flour in the muffin pan

Step 4: Fill the muffin pan with the pumpkin muffin batter. The batter will be thick. The longer it sits, the thicker it will get.

Tip: Silicon muffin pans, silicon muffin cups, or parchment liners work best, as keto-friendly baking items tend to be very sticky.

cream cheese filling for keto pumpkin cream cheese muffins in a clear bowl with thee beaters from the mixers crossed at the top sitting in it. There is a plaid fall colored napkin in the left top corner

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Step 5: To make the cream cheese filling, add the room temperature cream cheese, sweetener, and vanilla to a small bowl and beat with a mixer on medium until it is smooth.

Pumpkin Keto muffin with cream cheese filling before baking in a metal muffin tin in parchment paper liners.

Step 6: Spoon the cream cheese filling mixture into the center of the muffin batter, then use a knife or toothpick to swirl the cream cheese into the batter a bit.

low carb muffins out of the oven in muffin tin

Bake until cooked through, then cool on a cooling rack.

Tips for Making Low-Carb Pumpkin Muffins:

  • Don’t be afraid of the spices. Pumpkin Pie spice is an incredibly delicious seasoning mix full of mouthwatering flavor. You can make it homemade if you can’t find pumpkin pie spice at your local grocery store.
  • This sugar-free recipe makes 18 regular-sized muffins. As Keto breads tend to stick to the pan, a silicone muffin pan or parchment paper liners are necessary. 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. Still, 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).
  • This recipe uses Wholesome Yum Monkfruit with Allulose blend Lakanto Monkfruit sweetener. You can substitute with Lakanto Monkfruit powdered or  Swerve Confectioners at the same measurement.

Can I make this recipe dairy-free?

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

  • Substitute Full Fat Coconut Milk for Heavy Whipping Cream
  • Substitute coconut oil for butter
  • Use dairy-free cream cheese to use in place of regular cream cheese.

What are some common mistakes people make when making keto pumpkin muffins?

One common mistake is using too much coconut flour, which can result in dry and crumbly muffins. Be sure to measure accurately and use the amount called for in the recipe. Another mistake is not using enough sweetener, which can result in bland muffins. Finally, be careful not to overmix the batter, as this can cause the muffins to be tough and dense.

Can I make pumpkin spice homemade?

You can make homemade pumpkin spice yourself by combining ground cinnamon, ground ginger, ground nutmeg, allspice, and cloves.

How to Store

After baking your delicious keto pumpkin cream cheese muffins, you’ll want to make sure they stay fresh for as long as possible. Here are some tips on how to store them properly:

Refrigerator: If you want to keep your muffins for longer, you can store them in the fridge for up to a week. Make sure to wrap them tightly in plastic wrap or aluminum foil before placing them in the container to prevent them from absorbing any unwanted flavors.
Freezer: To keep your muffins fresh for even longer, you can store them in the freezer for up to 3 months. Wrap each muffin individually in plastic wrap or aluminum foil before placing them in a freezer-safe container. When ready to eat them, thaw them at room temperature or in the microwave.
Reheated: If you want to enjoy your muffins warm, you can reheat them in the microwave or oven. To reheat in the microwave, place the muffin on a microwave-safe plate and heat for 10-15 seconds. To reheat in the oven, preheat your oven to 350°F (175°C) and bake for 5-10 minutes.

Tip: Remember to always let your muffins cool completely before storing them. This will prevent condensation from forming and making them soggy.

keto pumpkin muffins with a bite taken out

Variations to This Recipe:

If you’re looking to switch things up, there are plenty of variations you can try. Here are a few ideas to get you started:

Add chocolate chips: For a little extra sweetness and texture, try adding some sugar-free chocolate chips to your muffins. You can also try using dark chocolate chips for a richer flavor.
Mix in nuts: Chopped walnuts, pecans, or even pumpkin seeds can add some crunch and healthy fats to your muffins. Just be sure to watch your portion sizes, as nuts can be high in calories.
Use a different sweetener: While this recipe uses Wholesome Yum Monkfruit Allulose Blend, you can try using other keto-friendly sweeteners like Wholesome Yum Allulose. Just be sure to check the conversion rate, as different sweeteners may require different amounts.
Make mini muffins: If you’re looking for a bite-sized snack, try making mini muffins instead of full-sized ones. Simply adjust the baking time accordingly.

Don’t forget to add a side of protein with sausage cooked in the oven or air fryer.

These are just a few ideas to get you started. Don’t be afraid to get creative and come up with your own variations!

More Keto Pumpkin Recipes:

low carb pumpkin cream cheese muffin with a bite taken out of it
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4.61 from 225 votes

Keto Pumpkin Muffins with a Cream Cheese Filling

Indulge in the comforting flavors of fall with our moist and fluffy keto pumpkin muffins with a cream cheese swirl! Bursting with rich pumpkin spice flavor, they are baked to perfection using pumpkin puree and coconut flour, making them a perfect low-carb breakfast, dessert, or snack. 
Prep Time10 minutes
Cook Time20 minutes
Total Time30 minutes
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:


  • Begin by preheating your oven to 350°F. This step ensures that your muffins bake perfectly.
  • Prepare your muffin tins by greasing them lightly or lining them with muffin liners. This prevents the muffins from sticking.
  • In a microwave-safe bowl, melt the 1/2 cup of coconut oil and the 2 tablespoons of butter until they become a smooth liquid. Alternatively, you can also use liquid coconut oil.
  • Now, let's move to the main mixture. In a large bowl, crack open the 5 eggs and add them in. Pour 1 1/2 cups of Lakanto Monkfruit Powdered, 1 cup of pumpkin puree, 1 1/2 teaspoons of vanilla, and 1 tablespoon + 1 teaspoon of pumpkin pie spice. Mix these ingredients thoroughly, ensuring they are well combined.
  • Slowly introduce the melted coconut oil and butter into the mixture. Blend everything together until you achieve a consistent batter.
  • For the dry ingredients, add 1/2 teaspoon of salt, 1 1/2 teaspoons of baking powder, and 1/2 cup + 2 tablespoons of coconut flour into the bowl. Gently mix everything until there are no visible lumps and the batter is smooth.
  • Take your prepared muffin tins and carefully spoon the batter into each cup, filling them about 2/3 full.
  • To make the cream cheese filling, grab a separate bowl. Combine the following ingredients: 2 tablespoons of Lakanto Monkfruit Powdered, 1/4 cup of cream cheese (softened), and 1/2 teaspoon of vanilla. Stir these ingredients together until they form a smooth mixture.
  • Next, add an extra touch of deliciousness by placing approximately 1/2 teaspoon of the cream cheese filling on top of each muffin. Use a toothpick to gently swirl the cream cheese into the batter, creating a marbled effect.
  • Place your muffin tins in the preheated oven. Allow them to bake for around 18 to 22 minutes. To check if they're done, insert a knife into a muffin; if it comes out clean, they're good to go. However, remember that oven times can vary, so keep an eye on them.
  • Once they're ready, carefully remove the muffins from the oven and let them cool a bit before enjoying your delicious keto pumpkin muffins!



The carbs and fiber from the keto-friendly sweetener are not included in the nutritional info as most subtract to calculate 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. 
How to Store Low-Carb Pumpkin Muffins
After baking your delicious keto pumpkin muffins, you'll want to make sure they stay fresh for as long as possible. Here are some tips on how to store them properly:
Refrigerator: If you want to keep your muffins for longer, you can store them in the refrigerator for up to a week. Make sure to wrap them tightly in plastic wrap or aluminum foil before placing them in the container to prevent them from absorbing any unwanted flavors.
Freezer: To keep your muffins fresh for even longer, you can store them in the freezer for up to 3 months. Wrap each muffin individually in plastic wrap or aluminum foil before placing them in a freezer-safe container. When you're ready to eat them, simply thaw them at room temperature or in the microwave.


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



  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.

    2. The squash _type_ labeled “pumpkin” can vary between brands. Oddly, what Libby sells as “pumpkin” isn’t even what many think of as pumpkin.

      So in this case, the brand could matter more.

      I know, who would’ve guessed?!

  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.


4.61 from 225 votes (181 ratings without comment)

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