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

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.

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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4.62 from 218 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:

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


  • 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!


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  1. Hi! My teenage daughter is on a low carb diet and really wants to try these! Do you know if we could use canola oil rather than coconut oil? We really do not like coconut.

    1. 5 stars
      For keto you want to avoid vegetable oils so I would also recommend Avocado oil if strict keto. Canola oil is not keto and you want to avoid that in any ingredients 💕

  2. How much batter per cupcake liner? I only ask because I’m tracking my macros and I need to make sure to measure it out correctly to track the macros you posted 🙂

    1. Okay 😊 I’ll try it out and see what happens lol.
      Do you happen to have a cookbook?

  3. Can I use another flour and oil? I really do not like coconut at all. And in most recipes, is it ok to use almond flour rather than Coconut flour or oil.?

    1. You can sub almond flour but you’ll need 4x as much. You could try butter for the coconut oil.

  4. 5 stars
    I’m on a low carb diet and I got tired of eggs so I wanted to try something different, these are amazing very tasty, the texture is different than a regular muffin but still very good…

  5. Is it possible to use regular granulated Lakanto Monkfruit Sweetener in place of the powdered version? If so, do you have a recommended measurement?

    1. If you have an electric coffee grinder, you can use it to powder the sweetener, if desired.

    2. If you put the granulated sugar in a blender and mix it, it will turn into powered sugar.


    4. All of the recipes on my site are free, and each post has a jump to recipe button at the top of the page. It takes thousands of dollars to run my site per month; without those ads, that would not be possible. Just like anyone else who works to earn a paycheck, I do as well. Without those ads, my family would be in the hole every month and would likely go bankrupt due to the costs associated with running my site and all that is involved. People who help me would lose their jobs because I could not afford to pay them. That is why cookbooks cost money because there are no ads. There has to be some kind of exchange. Just as I’d never expected anyone to altar their job for my convenience, I would hope that others would realize that this is a full-time job for me, and you’ve never been required to pay one dime to access any of the recipes I’ve spent hours developing. Each recipe takes a minimum of 12 hours from development to posting and involves several assistants that help me such as a photographer/videographer, SEO researcher, and more. I know most people have no idea what goes into running a blog as I don’t know what goes into other peoples’ professions. Yes, I have to make a living just like anyone else otherwise there I would just spend time with my family.

  6. These are so delicious 😋
    I substituted the sweetener for caster sugar (but use half the amount).
    Can you tell me if it’s ok to freeze these and if so, for how long?

  7. 5 stars
    I made these last night and they are toddler approved and absolutely delicious! I did not have the powdered Lakanto, just their regular substitute so I used 1cup of that, and we were out of heavy whipping cream so I subbed some sugar free pumpkin spice creamer! So yummy and we can’t stop eating them!

    1. 5 stars
      So yummy. Mine took almost 40 minutes to bake all the way through, but my oven is wonky. Also used some of the batter in my mini dash and yummy!!!

    2. So glad you enjoyed them. Oven baking time can vary for sure. What a great idea to make some in the mini dash.

  8. 5 stars
    These muffins ARE. FREAKIN’. DELICIOUS. Needed a full 30 minutes in my oven, though the thermometer I have in there said 350. Will *definitely* make these again and bake at “my” 375 or 400 next time. Thank you, Kasey, this recipe is another winner!

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