Keto Pumpkin Muffins with Cream Cheese

by Clean Keto Lifestyle

These Keto Pumpkin Muffins with Cream Cheese are the perfect Fall treat! They are the perfect combination of pumpkin spice, tangy cream cheese, and sweet vanilla. These muffins are keto, low-carb, grain-free, and gluten-free!

Keto pumpkin muffins with cream cheese

Keto Pumpkin Muffins

Fall is officially here, which means it is all things pumpkin spice!

You know those pumpkin muffins that taste like sweet autumn time? That's these. First, you bite into the pumpkin spice that feels so comforting and warm. Then, the soft cream cheese filling.

It's like a cheesecake and a muffin all in one warm handheld pastry.

And it's keto-friendly too!

If you have a craving for something sweet while you are on keto, reach for these keto pumpkin muffins with cream cheese.

Keto pumpkin muffins with cream cheese

How to Make Keto Pumpkin Muffins

This is the only keto pumpkin muffin recipe you need. It tastes like fall feels.

These are entirely homemade, so the ingredient list is pretty long (but most of the items are probably in your kitchen already).

If you can make a boxed muffin mix, you can make these.

We also have some step-by-step pictures that will help you see the entire process.

After you make them, you'll want to share them with everyone! Even people who don't eat keto will gobble them up.

Clean Keto Pumpkin Muffins with Cream Cheese

Featured Recipe Video

Check out this video to see how to make our most popular recipe – Keto Zucchini Bread Whoopie Pies.

They are easy to make and so delicious!

Gather Your Ingredients

Here's what you'll need before you begin baking.

Pantry Staples:

Refrigerated Items:

What Equipment You Need

These keto muffins are super moist and so delicious. You are going to adore them! Here is a step-by-step guide to making them.

Clean Keto Pumpkin Muffins with Cream Cheese

Prepare the Batter

First, mix together the dry ingredients in a large mixing bowl.

Next, use an electric mixer to beat in the softened butter. Now the batter is going to look like coarse sand.

In a separate bowl, beat together the wet ingredients.

Then, beat the wet ingredients with the dry ingredients to make the muffin batter.

Clean Keto Pumpkin Muffins with Cream Cheese 0

Add the Pumpkin Batter to Your Muffin Tin

Now line your muffin tin – you need a 12-cavity one or two 6-cavity tins. Use either silicone or paper cupcake liners.

Fill each cupcake liner about 2/3 full with the batter (use about a 1/4 cup for each one). Don't overfill them.

Make sure to reserve some of the batter (a cup or so) in a small bowl. You will use the rest of the batter later as a topping.

Clean Keto Pumpkin Cream Cheese Muffins

Create A Cavity in the Batter

Use the back of a spoon or your finger to create a crater or small divet in the batter.

You want it to be big enough to add in your cream cheese mixture.

Speaking of cream cheese – it is time to make your filling.

In a separate medium bowl, use an electric mixer to beat together the cream cheese, confectioner erythritol, and vanilla extract until combined.

Clean Keto Pumpkin Cream Cheese Muffins - batter with a small hole in the middle for the cream cheese filling

Fill the Hole with Cream Cheese Mixture

Now add in about 1 1/2 teaspoons of the cream cheese mixture into each cavity you made for each pumpkin muffin.

Don't use all of it, save some for the topping.

cream cheese filling inside pumpkin batter for muffins

Add the Rest of the Batter

Next, take the rest of the pumpkin batter that you reserved in a small bowl and spoon a small dollop to the top of each muffin.

It doesn't have to cover the cream cheese fully.

Clean Keto Pumpkin Cream Cheese Muffins batter inside a muffin tin

Top with the Rest of the Cream Cheese Mixture

Now add another tiny bit of the cream cheese mixture on top of the pumpkin batter topping.

Use a toothpick to swirl them together.

Clean Keto Pumpkin Cream Cheese Muffins

Bake the Muffins

Put the pumpkin muffins in the oven and let them bake.

Bake for 18-20 minutes 350°F or until the muffins are golden brown on top.

This is the best part! Your entire house will smell like pumpkin spice!

Clean Keto Pumpkin Muffins with Cream Cheese

Keto Pumpkin Puree

Is pumpkin puree keto? Yes, it is (in moderation)!

Pumpkin is loaded with fiber, potassium, and vitamin C, which are great for a Clean Keto Lifestyle.

However, pumpkin is a squash and it does have carbs in it – approximately 5 grams per ½ cup.

As long as you don't overdo it, pumpkin can absolutely be a part of your keto diet.Keto pumpkin muffins with cream cheese

Keto Pumpkin Muffin Nutrition

At the bottom of this post, we included a nutrition facts label. Rest assured, these pumpkin muffins will fit into your keto macros, just watch how many you eat.

There are 20 grams of fat in them. Most of it comes from the cream cheese.

And there are only 4.7 net carbs in each muffin making these very keto-friendly!

Clean Keto Pumpkin Cream Cheese Muffins

How To Make Your Own Pumpkin Pie Spice

Pumpkin pie spice is one of those pre-made spices that you can buy online or at the grocery store. This will save you a bit of time.

Our favorite one is from Primal Palate. It is organic and has no added fillers or sugar.

But if you want to make you own, you can just combine the following spices together:

Store this spice mixture in a sealed container at room temperature for up 6 months.

Clean Keto Pumpkin Cream Cheese Muffins

Other Keto Desserts To Try

After one bite, these will become one of your favorite fall treats. If you are looking for other great autumn sweets, try these other keto desserts, you'll love them too.

Clean Keto Pumpkin Cream Cheese Muffins

How to Freeze Pumpkin Muffins

These muffins freeze beautifully. Then when you are ready to thaw them and eat them, just pull one out and leave it in the refrigerator overnight.

To freeze the muffins, let them cool completely first. Then, wrap them up individually in plastic wrap. Place the muffins in a plastic bag or another freezer container.

Re-heating them is simple. Let them thaw overnight in the refrigerator. Then heat them in the oven.

To do that, wrap them in parchment paper and place them in a 350°F oven for 10-15 minutes.

Clean Keto Pumpkin Cream Cheese Muffins


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Leave a Comment


rachael September 26, 2019 - 3:14 pm

has anyone actually made these? I’m so tired of making treats and they turn out horrible. Please comment if you have made them and how they taste!

Jennifer Hubbard October 6, 2019 - 10:39 am

I made these last week and I am about to make more today. My family loved them! They aren’t very sweet but have a lovely buttery taste to them . We are cream cheese junkies so we love anything with cream cheese. I didn’t notice a much of a pumpkin taste. I may need to add more spices. You can also add more swerve to the batter if you like them sweeter.

Mandy October 11, 2019 - 12:44 pm

Not sure what I did wrong with these. The flavor is outstanding but I cooked them a good 30 minutes and they never cooked all the way through. They also sank a considerable amount in the middle so they all have large holes in the center. A bummer… After all the ingredients and time.


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