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Cream Cheese Keto Pumpkin Muffins

Delicious keto pumpkin muffins bring the spiced fall pumpkin breezes to your kitchen. The perfect low carb breakfast packed with cream cheese, pumpkin spice, and sugar-free chocolate chips.

Keto pumpkin muffins on a plate

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Oh, the cool, breezy fall mornings! How I love colder weather coming in and the leaves floating to the ground. Really, it’s about time. Summer, it’s time to part ways.

Yesterday, my kids harvested our crop of jack-be-little decorative pumpkins. While we don’t have a huge space for a garden, I think they counted up 25 decorative pumpkins. Also, we managed not to kill 5 pie pumpkins, score.

What this means is that we’re in full pumpkin spice recipe joy mode!

Flavorful keto pumpkin muffins will get your taste buds ready for fall. A delicious low carb breakfast packed with pumpkin spice, cream cheese, and sugar-free chocolate chips. #ketobreakfast #lowcarbmuffins #ketorecipes

While I think you’ll love my super helpful tips and fun stories, I also realize we are sometimes pressed for time and just need a good recipe!

Scroll down to the bottom of the page for the printable recipe or PIN it here for later!

I’m so glad I live in a world where there are Octobers.

– Lucy Maud Montgomery, Anne of Green Gables

Why make pumpkin purée

Do you make your own pumpkin purée for baking or use it out of a can? Growing up, my father would gasp in horror if you even mentioned canned pumpkin.

“It just has NO flavor,” and we all would shake our heads feeling sorry for those unfortunates who had to use canned pumpkin.

Actually, to make your own purée is pretty easy and can be hugely rewarding.

How to make pumpkin purée

First, all you do is cut the pumpkin (we call them pie pumpkins) in half. If you have one from your own garden, all the better!

Remove the gooey insides. Also, don’t forget to save the seeds and salt and toast them to snack on later!

Second, place each pumpkin half open-side down on a baking sheet. They’re placed this way so the air and moisture are trapped inside the pumpkin to steam as it bakes.

Then place the baking sheet with pumpkin halves in a 350 degree (Fahrenheit) preheated oven for about an hour.

To test the pumpkin, pull it out of the oven and lightly tap on the outside skin. The inside pumpkin flesh should be soft and start to fall away from the skin.

Next, turn the pumpkin halves over and spoon the soft pumpkin insides into a good blender or food processor.

Lastly, process the pumpkin for about 40 seconds until it becomes a smooth purée.

If you use a blender you may have to push the pumpkin down into the blades several times to completely process. Just be sure to turn off the blender to do this unless it has a special tamper for that purpose!

Overhead view of six keto pumpkin muffins on a plate

🍽 Equipment

To make keto pumpkin muffins you’ll need:

Hand holding one keto pumpkin muffin

“Hello, gourd-geous.” 

– Unknown

🥘 Ingredients

🔪 Instructions

How to make keto pumpkin muffins

Let’s begin like we always do. Get out all ingredients and kitchen utensils so everything is close at hand.

Second, preheat the oven to 325 degrees Fahrenheit. This is the temperature I find works best for baking gluten-free muffins and cakes.

Now crack the eggs into a large bowl. Then add in the pumpkin puree, vanilla, sweetener, and almond milk. Mix it together evenly using a hand-held or standing mixer.

Next, take out another bowl, and whisk together the almond flour, coconut flour, salt, baking powder, and pumpkin pie spice.

Don’t forget to take a moment to breathe in and enjoy that pumpkin pie spice!

How to make pumpkin pie spice

TIP: If you don’t have pumpkin pie spice, you can substitute two teaspoons of cinnamon, one teaspoon ground ginger, half a teaspoon nutmeg, and one-half of a teaspoon ground cloves.

Next, add the wet ingredients to the dry and combine them together well with a mixer or spatula.

Now it’s time to measure in 1/2 cup of the sugar-free chocolate chips. Don’t pour them all in! Save the rest to sprinkle on top to make the muffins pretty. Nothing says pretty like chocolate!

If you haven’t already, now’s the time to prepare a muffin tin with liners or grease with butter or coconut oil.

Cream cheese topping

Then prepare the filling. It’s super quick and easy. Simply mix together the cream cheese, heavy cream, and powdered sweetener with a mixer for about 2 minutes. Boom, done!

💭 Top tip

My favorite tip when baking keto pumpkin muffins is to use an ice cream scoop.

An ice cream scoop?!

Yes, indeed. An ice cream scoop is the perfect way to evenly and quickly distribute the batter in the muffin cups.

To assemble, first, fill the twelve muffin cups until the batter is evenly distributed.

Next, spoon a generously rounded teaspoon of cream cheese mixture on top of the batter in each muffin. Take a toothpick and swirl the cream cheese into the pumpkin muffin batter.

Toothpick is used to swirl cream cheese into the keto muffin batter

To finish it off, sprinkle the tops with about 5 sugar-free chocolate chips each. Nice!

⏲️ Baking time

Finally, bake them off in the 325-degree oven for 25-30 minutes. I start checking the oven around 22 minutes.

There are many factors at play with bake time – the specific ingredients, your altitude, and even the oven. The best advice it to keep an eye on them.

Cool in the pan for at least 10 minutes then remove the muffins to racks to cool completely.

Overhead view of baked keto pumpkin muffins

🥣 How to store keto pumpkin muffins

As with any gluten-free baked good, store in an air-tight container. Also, they are best kept chilled rather than on the counter.

They’ll keep in the refrigerator for about a week or up to a month in the freezer.

I like to freeze a batch to have them ready for a quick on the go breakfast!

👩‍🍳 Variations

1. Fill the muffin with the cream cheese mixture instead of putting it on top.

Cream cheese keto pumpkin muffins are low carb delish. Perfect for a quick grab-and-go keto diet breakfast with fall spice and sugar-free chocolate chips. #lowcarbbreakfast #ketorecipes #ketobreadfast

As before, prepare a muffin tin with liners or grease with butter. However, then place 2 tablespoons of batter in the bottom of each muffin tin round.

Then, spoon a rounded teaspoon of the cream cheese mixture on top of the batter in each muffin cup.

After that, top each muffin evenly with the rest of the muffin batter. Now sprinkle the tops with the remaining sugar-free chocolate chips. Bake as directed.

Cream cheese filling makes a divine keto pumpkin muffin! These low carb babies make a delicious grab-and-go sugar-free breakfast, perfect for fall or anytime! #ketorecipes #pumpkinspice #lowcarbpumpkin

2. Leave off the cream cheese topping/filling completely.

If you don’t want to deal with the filling. First get out your blender. I love using my Vitamix blender for baking.

Instead of a bowl, place all the wet ingredients in the blender. Then simply blend the 4 ounces of cream cheese from the filling in with the wet ingredients.

Easy delicious keto pumpkin muffins. The perfect low carb breakfast and filled with cream cheese, pumpkin spice, and sugar-free chocolate chips. #ketobreakfast #ketomuffins #lowcarbbreakfast

Leave out the extra heavy cream and sweetener called for in the filling.

Mix the wet and dry ingredients and fill the muffin cups about 3/4 full to bake as instructed.

This makes delicious and moist pumpkin spice muffin, just without the filling!

Fall pumpkin spiced low carb muffins are the perfect keto breakfast. Sugar-free chocolate chips, cream cheese, delish! #ketorecipes #ketobreakfast

🎃 Do you love fall pumpkin spice?

I love ALL things fall and am in heaven with these first few days of October in sweaters. Sweaters, scarves, yellow aspen leaves, and pumpkin spice. Bliss.

The heater even turned on this morning, which I promptly turned off.

The little pumpkin decorative pumpkin gourds from the garden are now spread throughout the house. Also, October means I’m free to go hog-wild with the baking! 

You might have to tell me to rein it in a bit, but let me tell you something.

Enjoy it. Enjoy your baking and this magnificent season. 

If you’re following a keto diet, just watch your macros and figure out what works for you.

I’m all about fitting in what brings me joy, and baked goods with pumpkin spice definitely fall into that category!

Pin the recipe here

Cream cheese keto pumpkin muffins are easy and low carb delicious. Packed with pumpkin spice, sugar-free chocolate chips, and cream cheese, your taste buds, and your keto diet, will thank you. #ketodiet #ketorecipes #ketobreakfast

Tag me in your recipe pics on Instagram @explorermomma.

If you LOVE this recipe please consider giving it a five-star rating in the review area below!

📋 Other keto fall spice recipes

  1. Best Ever Keto Spice Cake
  2. Easy Whipped Keto Pumpkin Mousse
  3. Low Carb Cinnamon Pecan Cookies
  4. Keto Pumpkin Scones
Keto Pumpkin Muffins on a plate

Keto Pumpkin Muffins

Yield: 12
Prep Time: 15 minutes
Cook Time: 25 minutes
Total Time: 40 minutes

Delicious keto pumpkin muffins are filled with cream cheese, pumpkin spice, and sugar-free chocolate goodness. The perfect low carb breakfast.

Ingredients

  • 4 eggs
  • 1/2 cup pumpkin puree
  • 1 tsp vanilla
  • 1/2 cup unsweetened almond milk
  • 1/2 cup sweetener, such as Swerve, 1/2 to 3/4 cup depending on how sweet you prefer
  • 2 cups blanched almond flour, finely ground
  • 1/4 cup coconut flour
  • 1/4 tsp salt
  • 2 tsp baking powder
  • 1 tbsp pumpkin pie spice
  • 3/4 cup sugar-free chocolate chips (optional)
  • 4 oz cream cheese, room temperature
  • 2 tbsp heavy cream
  • 2 tbsp powdered sweetener, such as Swerve Confectioners

Instructions

  1. Preheat the oven to 325 degrees Fahrenheit.
  2. Place the eggs, pumpkin puree, vanilla, sweetener, and almond milk in a large bowl. Mix thoroughly using a hand-held or standing mixer.
  3. In another bowl, whisk together the almond flour, coconut flour, salt, baking powder, and pumpkin pie spice.
  4. Add the wet ingredients to the dry and combine well with a mixer or spatula.
  5. Pour in 1/2 cup of the sugar-free chocolate chips. Save the rest to sprinkle on top.
  6. Prepare a muffin tin with liners or grease with butter or coconut oil. Use a spoon or ice cream scoop to evenly distribute the muffin batter.

Cream Cheese Topping (or filling)

  1. Mix together the cream cheese, heavy cream, and powdered sweetener with a mixer for about 2 minutes.
  2. Before baking, spoon a well-rounded teaspoon of cream cheese mixture on top of each muffin.
  3. Top with the remaining sugar-free chocolate chips.
  4. Bake in the 325-degree oven for 25-30 minutes. Cool in the pan for 10 minutes then remove the muffins to racks to cool completely.

Notes

*TIP* If you don't want to deal with the filling simply blend the 4 oz of cream cheese in with the wet ingredients and leave out the extra heavy cream and sweetener. Mix the wet and dry ingredients and fill the muffin cups about 3/4 full to bake. This makes delicious and moist pumpkin spice muffin, just without the filling.

Nutrition Facts

Servings 15.0 Amount Per Serving: 1 muffin Calories 135  Total Fat 11 g Saturated Fat 4 g Monounsaturated Fat 3 g Polyunsaturated Fat 1 g Trans Fat 0 g Cholesterol 60 mg Sodium 163 mg Potassium 86 mg Total Carbohydrate 7 g Dietary Fiber 5 g Sugars 1 g Protein 4 g Net Carbohydrate 2 g

Nutrition Information:
Yield: 15
Amount Per Serving: Calories: 195Total Fat: 16gTrans Fat: 0gCarbohydrates: 7gNet Carbohydrates: 4gFiber: 3gProtein: 7g

*Nutrition Facts per MyFitnessPal.com. For most accurate facts, calculate your own with the exact ingredients you use in the recipe.

Did you make this recipe?

Tag @explorermomma on Instagram and hashtag it #explorermomma. Thanks a bunch!

NUTRITION DISCLAIMER

Please be aware I am not a medical specialist or nutritional professional. On this blog, I share recipes and what works for me. Please do not take anything on this blog as medical advice and always consult with your doctor before starting any diet or exercise program.
 
I use MyFitnessPal.com to calculate nutrition facts as a courtesy to my readers, and I remove erythritol from the final carb count and net carb count because it does not affect my own blood glucose levels.
 
This is as accurate as possible, but it’s best to independently calculate nutritional information on your own with the specific ingredients you use.
 
I expressly disclaim any and all liability of any kind with respect to any act or omission wholly or in part in reliance on anything contained in this website.

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