These Pumpkin Cream Cheese Swirl Muffins are loaded with warm pumpkin and vanilla flavors, making them the quintessential fall treat. They are perfectly moist and fluffy, with a cream cheese swirl that makes them extra special.

❤️ Why You’ll Love This Keto Pumpkin Cream Cheese Muffins Recipe

• Sweet and delicious pumpkin 
• Warm pumpkin pie spice
• Cream cheese vanilla swirl
• Baked into the most incredible muffins
• Moist and perfectly fluffy texture
• Gluten-free, sugar-free and kid friendly

Nothing spells fall like the smell of something pumpkin baking in the oven. When you make these muffins, your kitchen will smell absolutely incredible! But better than that, they taste amazing and are really so easy to make.

These low carb pumpkin muffins are moist, yet fluffy and have just the right amount of sweetness. And because I use a brown sugar-free sweetener in them, they have a molasses or slight hint of caramel flavor that makes them taste incredible. I also use my homemade pumpkin spice which just sends them over the top. It’s essentially fall in a muffin!

They’re great for a grab and go breakfast or late afternoon snack. And the good news is, since this recipe uses canned pure pumpkin puree, you can whip up a batch all year long, so you don’t have to wait for the fall!

🛒 Ingredients for Low Carb Pumpkin Muffins

• Super fine almond flour
• Pumpkin puree
• Brown monk fruit/allulose
• Monk fruit/allulose, powdered
• Cream cheese
• Heavy cream
• Oat fiber
• Eggs
• Baking powder
• Pumpkin Pie Spice
• Vanilla extract

*Exact measurements are listed in the recipe card below.

🥣 Recommended Tools

• Mixing bowls
• Whisk
• Hand mixer
• Ice cream scoop
• Piping bag
• Muffin pan
• Muffin liners

🔪 How to Make Gluten-Free Pumpkin Muffins

Preheat oven to 350°F.

To Make the Pumpkin Muffins

Add the almond flour, oat fiber, baking powder, pumpkin pie spice and salt to a small mixing bowl.  Whisk to combine, then set it aside.

In a separate mixing bowl, add in the eggs, pumpkin puree, heavy cream, brown sweetener and vanilla extract.  Mix using a hand mixer until well combined.

Add the dry ingredients into the wet and mix just until combined, don’t over mix it.

Using an ice cream scoop or spoon, add the batter into 12 muffin liners in a muffin baking pan.

To Make the Cream Cheese Swirl

In a small mixing bowl, add in the cream cheese, heavy cream, sweetener and vanilla extract.

Mixing until combined, then add it to a piping bag and cut off the tip.

Pipe out small dots of the mixture over and into the pumpkin muffin batter.

Take a toothpick or butter knife and gently swirl the cream cheese into the batter, creating little swirls.

Bake for 22-25 minutes or until a toothpick when inserted, comes out clean.

Allow to cool to room temperature before serving.

☑️ Storage Instructions

Store leftovers muffins in an airtight container in the fridge for up to 5 days or freeze.

💡 Tips for Making Pumpkin Muffins

• It’s important to whisk the dry ingredients together, as this not only combines them but it also helps to break up any lumps.
• I like to use an ice cream scoop to make ensure the muffins are all the same size and takes the same amount of time to bake. If you don’t have one, you can use a spoon instead.
• Using a piping bag makes it easier to add small dollops of the cream cheese mixture into the pumpkin muffin batter. If you don’t have a piping bag, you can use a food storage bag instead and just cut off the tip.
• Creating the swirl using a toothpick is the easiest way to do this, but you can also use the tip of a knife. I find the toothpick gives you a better swirl, just be sure not to overdo it, or you will just be blending it and will lose that swirly look.
• These muffins take a little longer to bake than some muffins, and ovens can also vary a little in cooking times. Using the “insert toothpick” method is always best. If it comes out clean, you’re good to go, but if there are wet crumbs, they need to bake a little longer.

🔄 Substitutions and Additions

• Be sure to use pure pumpkin puree in the can, not to be confused with pumpkin pie filling. This also means you can make these muffins year round, which is great. But if it’s pumpkin season and you happen to have an excess of pumpkin, you can certain make your own puree and use it instead.
• If you really want to ramp up the vanilla flavor in the cream cheese swirl, you can use a little vanilla bean paste instead of the extract. I’d use about half the amount, as it’s much more concentrated than the extract.
• Always use full-fat cream cheese in Keto baking. If you don’t like the taste of cream cheese, but still want the vanilla flavored swirl, you can use mascarpone cheese instead of the cream cheese. It’s milder in flavor and even has fewer carbs.
• If you want to skip the swirl all together, you certainly can, just omit those ingredients and bake the pumpkin muffins as it. Or you can add in some sugar-free white chocolate chips for a little added sweetness.  Or if you like nuts, you can add in some pecans, almonds or walnuts.  Just be sure to chop them up first.

What is the secret to moist pumpkin muffins?

Using a decent amount (1 whole cup in this recipe) of pumpkin puree is key. Also using heavy cream also helps keep them nice and moist as well.

Are pumpkin muffins actually healthy? Are keto muffins actually healthy?

Traditional pumpkin muffins that use all purpose flour and sugar are not healthy. But these muffins, that use almond flour and sugar-free sweeteners which are Keto friendly most certainly are! They have only 3 net carbs each!

What’s the difference between pumpkin muffins and pumpkin cupcakes?

Pumpkin Cupcakes are fluffier and more cake-like, where this recipe for pumpkin muffins are a bit heavier and more dense (in a good way!).

Are muffins actually healthier than cupcakes?

In terms of traditional muffins yes, only because they are lacking the sugary frosting that is used on cupcakes. But whether you make these pumpkin muffins or my pumpkin cupcakes, they are both made using similar healthy and sugar-free ingredients.

🍽️ More Keto Pumpkin Recipes

• Pumpkin Coffee Cake
• Pumpkin Chaffles
• Pumpkin Donuts
• Fluffy Pumpkin Pancakes
• Pumpkin Muffins with Cream Cheese Filling
• Pumpkin Bulletproof Coffee