Enjoy these moist and creamy Low Carb pumpkin muffins that are topped with chopped roasted pecans!  They're loaded with pumpkin flavor and a sugar-free cream cheese filling in the center, making them so decadent!

Jump to:

• What's in Keto Pumpkin Muffins
• How to Make Keto Pumpkin Cream Cheese Muffins
• Is Pumpkin Keto?
• Tips for Making the Best Muffin Recipes Made with Almond Flour
• Additional Topping for These Low Carb Pumpkin Muffins
• More Keto Pumpkin Recipes
• What is Oat Fiber? Is Oat Fiber Keto?
• What is a Substitute for Oat Fiber?

You are in for a lot of pumpkin goodness with these delicious muffins! These gluten-free pumpkin muffins are moist, full of pumpkin flavor and stuffed with a sweet cream cheese filling.

The warmth from cinnamon in the spice mix in these muffins give them a homemade flavor that's perfect for the holidays.

This recipe used Homemade Pumpkin Pie Spice mix and an all time favorite Keto/low carb sweetener, Brown Swerve, which tastes and feels just like real brown sugar!  The cream cheese filling is similar to a frosting, but not quite as thick or sweet.  

These Keto muffins are topped with chopped pecans, which adds a great contrast in texture!

What's in Keto Pumpkin Muffins

• Super fine almond flour
• Oat Fiber 
• Eggs
• Pumpkin puree
• Sour cream
• Cream cheese
• Heavy cream
• Brown Swerve
• Swerve confectioners
• Baking powder
• Pumpkin Pie Spice
• Vanilla extract
• Salt
• Chopped pecans

*Exact measurements are listed in the recipe card below.

How to Make Keto Pumpkin Cream Cheese Muffins

To Make the Gluten Free Muffins

Preheat oven to 350F.

Add the almond flour, baking powder, oat fiber and salt to a bowl and whisk together, then set aside.

In a separate bowl, whip up the egg whites to soft peaks.

In another bowl, add the egg yolks, Brown Swerve and the other wet ingredients. Mix using a hand mixer or whisk.

Fold in the egg whites into the wet ingredients.

Then add the dry ingredients into the wet and mix just until combined.

Scoop the batter into silicone cupcake liners or muffin time with paper liners about ⅔ of the way up the sides. Place cupcake liners on a sheet pan.

To Make Sugar Free Cream Cheese Filling

Mix all the filling ingredients in a bowl, using a hand mixer.

Using a small scooper, about the size of a melon baller, add some of the filling in the center.

Cover with the remaining muffin batter.  Using a mini silicone spatula and water, smooth out the tops.

Top with roasted chopped pecans. You can uses walnuts instead if you prefer.

Bake for 18-20 minutes or until a toothpick when inserted comes out clean.

Allow to cool before serving.  These muffins are best served room temperature. Because of the cream cheese filling, store leftovers in the fridge for a few days or freeze.

To freeze leftover muffins, just wrap them individually in plastic wrap and place in the freezer for up to a couple of months. When you're ready to eat one, just unwrap it and put in on the counter for about 30 minutes until thawed.

Be careful reheating this in the microwave because the cream cheese will melt and ooze out. You don't want that!

Is Pumpkin Keto?

Pumpkin puree makes a delicious pumpkin pie filling and it is super nutritious! And the great news is a half cup is going to have 4.5 to 5 grams net carbs depending on the variety of pumpkin. That makes it an excellent low carb ingredient to add fall flavor to any recipe.

Tips for Making the Best Muffin Recipes Made with Almond Flour

Best Keto Baking Mixture

Baking with almond flour saves a lot on carbs and help to convert many high carb recipes into Keto versions. By adding in some oat fiber together with the almond flout it creates a really great light and fluffy texture you're looking for in baked goods.

Some recipes use coconut flour, but I find that the combination of almond flour and oat fiber keeps these low carb muffins moist and creates wonderful texture.

Best Keto Sweeteners for Keto Pumpkin Spice Muffins

There are several really good Keto friendly sweeteners that have little to no net carbs per serving. This recipe uses Swerve brand sugar substitutes.

Swerve comes in confectioners, granulated and brown. They all have amazing flavors, contain no artificial ingredients or preservatives. Plus, Swerve is zero-calorie, non-glycemic and does not affect blood glucose or insulin levels.

Additional Topping for These Low Carb Pumpkin Muffins

These muffins have a yummy creamy cheese filling that make them so rich and delicious but it you want add a little extra decadence, you can take a tablespoon of sugar free maple syrup and drizzle right over the cooled muffins. If you like to slightly warm your muffins before serving, you can top each one with a small pat of butter and allow it to melt into the muffins.

More Keto Pumpkin Recipes

If you love this Keto Pumpkin Muffin recipe, check out these other low carb pumpkin recipes:

• Pumpkin Coffee Cake
• Pumpkin Donuts with Maple Cream Cheese Icing
• Pumpkin Spiced Bulletproof Coffee
• Pumpkin Vanilla Swirl Cheesecake Bars
• Easy Pumpkin Cream Cheese Mousse
• Pumpkin Pie Fat Bombs
• Pumpkin Pancakes
• Pumpkin Cupcakes with Cream Cheese Frosting

What is Oat Fiber? Is Oat Fiber Keto?

Oat Fiber is made from grinding the outer husks of oats. How healthy is oat fiber? It's pure insoluble fiber, which doesn't dissolve in water and isn't broken down in the digestive tract, so it has zero net carbs and is perfect for a Keto Diet. It helps give a more traditional texture and that's why I use it so often. Check out all the Keto Oat Fiber Recipes you can make!

What is a Substitute for Oat Fiber?

To get the best results, it's best to use oat fiber if you can. If you're unable to find it, try a combination of psyllium husk powder and coconut flour. Since both are very absorbent, you might have to add more liquid.

If you'd like to know more about baking on Keto, this article, Keto Baking Made Easy, is loaded with tips and info that you'll find helpful. You might also check out my Keto Sweet Treats eBook that has 50 amazing Keto dessert recipes, all with color pics, macros and more! I'm offering it at 50% off when you subscribe to my free weekly emails here.