Dessert/ Recipes

Keto Pumpkin Spice Cream Cheese Muffins

Picture of 3 Keto Pumpkin Spice Cream Cheese Muffins on a plate with colored fall leaves for the blog keto on the rise

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Pumpkin Spice and all things nice! Whether you are team pumpkin spice or not, this weeks recipe for Keto Pumpkin Spice Cream Cheese Muffins will have you feeling right in the middle of the comforts of fall!

Each Keto Pumpkin Spice Cream Cheese Muffin has only 4 net carbs, with nice clean ingredients. Keep these muffins for yourself or share with a friend, these will be a hit keto or not!

My inspiration was not only this classic fall flavor, but my general love for baking and pretty desserts. While down at our lake house in Branson, Missouri we went to a local bakery and low and behold in the dessert case were these big beautiful pumpkin muffins. Not only were these muffins huge, they were filled with a swirl of cream cheese filling. Now, I have no idea (and really don’t want to know) how many carbs were in each of these muffins. However, I knew right then and there I would be making a keto version. So here is the recipe for Keto Pumpkin Spice Cream Cheese Muffins.

Basic Ingredients for a Keto Pumpkin Spice Cake

The ingredients for the pumpkin spice cake portion of the muffins are simple and come right out of your keto pantry using some of the best keto baking ingredients. If you want to know more about keto baking ingredients, check out this blog post!

What you will need for the cake portion of the muffins:

  • 12 muffin pan and muffin liners
  • Almond Flour-I prefer Bob’s Red Mill-Super Fine-4 pack
  • Swerve
  • Whey protein powder-I like IsoPure for baking! *See my next comment about baking with whey protein powder*
  • Baking Powder
  • Pumpkin Pie Spice
  • Salt
  • Eggs
  • Pumpkin Puree-NOT Pumpkin Pie filling, you are looking for plain pureed pumpkin
  • Butter
  • Heavy Cream
  • Vanilla

So this is the grocery list for all the ingredients for the base of our Keto Pumpkin Spice Cream Cheese Muffins. Before we talk about the cream cheese filling let me circle back to a few ingredients.

First, the whey protein powder. Please, don’t just throw in the towel when you see this ingredient. Whey protein powder is used in alot of keto baking. Folks, keto baking and carb/sugar loaded baking are just not the same. However, they can taste very similar with just a few tweaks and using whey protein powder in your keto baking is one way to do this. Whey protein powder not only gives you an extra boost of protein but also makes keto baked goods fluffy without using a bunch of eggs. We are not making an egg muffin here. We are making a bakery quality Keto Pumpkin Muffin. I linked the IsoPure unflavored protein powder above. It is reasonable in price and will last quite awhile!

Second, the pumpkin puree. Please make sure that you get the pumpkin puree which is just plain canned pumpkin without added ingredients, as opposed to Pumpkin pie filling which has spices and loads of sugar added to it. Check out the difference in the nutrition and ingredient labels while you’re at the store.

The Icing on the cake-literally……

And finally, the icing on the cake. What would these Keto Pumpkin Spice Cream Cheese Muffins be without the cream cheese frosting? This frosting is so simple and so delicious. Cream cheese, swerve, heavy cream and vanilla are the only ingredients required. Whip this frosting until it is nice and fluffy, we will pipe or spoon this into our muffins!

This basic cream cheese frosting would also be delicious on a keto carrot cake, keto red-velvet, keto spice cake, keto zucchini cake or keto brownies…..hello keto dessert deliciousness right?

To fill our keto muffins, after they have completely cooled, I use the base of a Wilton icing tip to make a hole in the center of the cupcake, but you could just use a scoop or a spoon to hollow out a bit of the center. Once you remove the center then pipe a bit of the cream cheese into the center of each cupcake, piping the cream cheese icing evenly into the 12 muffin ‘holes’. Place the ‘top’ back on the muffin and you have the cutest bakery worthy Keto Pumpkin Spice Cream Cheese Muffins.

There is everything to love about this simple but delicious fall keto baking recipe. It’s a muffin, it has icing, it’s pumpkin spice people! I have to admit I ate 2 muffins the first day, they can be tempting even on keto but as always…I can’t wait for you to try them!

If you know someone who loves keto baking or baking at all, please use the links in this post to share or Pin this recipe. I so appreciate your support of this blog and to learn even more about the keto lifestyle, keto recipes, tips and the story of my keto transformation, you can checkout the Facebook page Keto On the Rise.

Stay On the Rise,


Keto Pumpkin Spice Cream Cheese Muffins

Keto Desserts
By Sara Serves: 12
Prep Time: 15 min Cooking Time: 25 minutes Total Time: 40 minutes

There is everything to love about this simple but delicious fall keto baking recipe. It's a cupcake, it has cream cheese icing, it's pumpkin spice people!


  • For the muffins
  • 2 cups Almond Flour
  • 1/2 cup Granulated Swerve or keto friendly sugar substitute
  • 1/4 cup Whey Protein Powder(see note above on my favorite)
  • 2 tsp Baking Powder
  • 2 tsp Pumpkin Pie Spice
  • 1/2 tsp Salt
  • 2 Large Eggs
  • 1/2 cup Pumpkin Puree-canned
  • 1/4 cup Melted Butter
  • 1/8 cup Heavy Whipping cream mixed with 1/8 cup water=total 1/4 cup liquid (or 1/4 cup unsweetened almond milk)
  • 1/2 tsp Vanilla
  • For the Cream Cheese Icing
  • 8 oz Softened Cream Cheese
  • 3 Tablespoons Powdered Swerve
  • 1 Tablespoon Heavy Whipping Cream
  • 1/2 tsp Vanilla



Preheat an oven to 325 degrees


Line a 12 cup muffin tin with 12 muffin liners.


Mix all the ingredients for the muffin batter in a large bowl, then using a cookie scoop or spoon evenly divide the batter among the 12 muffin cups.


Bake at 325 degrees for 25 minutes or until the tops/edges of the muffins are slightly golden.


When the muffins are done, cool completely on a baking rack before icing.

For the cream cheese icing


Add the cream cheese, powdered swerve, heavy whipping cream and vanilla to a stand mixer or use a hand mixer.


Beat on medium high for 5 minutes allowing the icing to get nice a fluffy.


While the icing is mixing, use the base of a piping tip to make a hole in the center of the muffins as shown above....keep the 'top'!


Use a spoon or a piping bag fitted with a piping tip to fill the muffins, evenly dividing the icing among the 12 muffins.


Replace the 'top' of the muffin that you removed and enjoy your Keto Pumpkin Spice Cream Cheese Muffins!


  • 6g Carbohydrates
  • 2g Fiber


The muffins could be frozen without icing and could be iced later. They would also be delicious without the icing! You could add nuts to the batter, up to 1/2 cup. The carbs would increase slightly.


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