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Keto Pumpkin Muffins Recipe

This Keto Pumpkin Muffins with a Cream Cheese Swirl Recipe is going to be a go-to treat or breakfast in the fall. Pumpkin spice season hits, and this is a must in your recipe list! So easy, yummy, and perfect for that craving!

Keto Pumpkin Muffins with a Cream Cheese Swirl

When I posted my Low Carb Pumpkin Bread , I had no idea how popular it would be. I knew my family loved it, but everyone has different tastes, so you just don’t ever know what will happen when you publish a new recipe. I’ve gotten tons of incredible feedback. Mostly, I’ve heard that it’s not eggy at all or dry like most Keto or Low Carb bread.

I thought I’d change it up the recipe a bit to make Low Carb Pumpkin Muffin by adding a swirled cream cheese mixture to the batter and making a couple of other minor adjustments to the recipe. We all loved how it turned out! In fact, this morning for breakfast, my 19-month-old couldn’t get enough. She ate two muffins and asked for more.

As I shared in the Pumpkin Bread post, the recipes that I have adapted to Keto/low carb are a good 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 sweet treat.

These Keto Pumpkin Muffins with a cream cheese swirl and easy to make. You'll find them moist without being eggy and full of pumpkin deliciousness.

How to Make Keto Pumpkin Muffins

Below, I have included my step-by-step picture tutorial. If you want just the printable recipe, feel free to scroll to the bottom of the post.


I was able to make 18 regular sized muffins. I would suggest using muffin liners or parchment paper liners as Keto bread tend to stick to the pan. Personally, I love parchment paper muffin liners as they prevent the muffins from getting too wet on the bottom.

Low Carb Pumpkin Muffins

Spoon the cream cheese filling mixture in the center of the muffin batter.

Low Carb Pumpkin Muffins

With a toothpick or a knife, swirl the cream cheese filling into the pumpkin batter.

More Recipe Ideas & Resources

Keto Pumpkin Muffins

Pumpkin Cream Cheese Muffins {keto friendly/low carb}


For the Muffins:

For the Filling:

  • 3 oz cream cheeseroom temperature
  • 1 table spoon heavy whipping cream
  • 1 1/2 tablespoon Swerve Confectioners
  • 1/2 teaspoonvanilla


  • Melt coconut oil and butter. ( I have started using liquid coconut oil for baking).
  • Beat eggs, swerve, 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 muffin liners 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 Swerve 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.
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