Keto Pumpkin Cheesecake Muffins

These keto pumpkin cheesecake muffins are sure to become a seasonal favorite.

Bursting with the fall spices we crave, filled with a cheesecake filling, and topped with a streusel crumb, they make the perfect breakfast or anytime snack!

I already have a few pumpkin muffins/cupcakes that are favorites around here, like my keto pumpkin cream cheese cupcakes and keto pumpkin streusel cupcakes. 

But these are almost in a class all by themselves. It’s like having three muffins in one!

Every year I look forward to pumpkin season, and I can’t resist the urge to keep creating keto-friendly pumpkin recipes.

It’s like a pumpkin spice alarm goes off in my brain and all I want is to create more and more pumpkin options for you.

In fact, our collection of keto pumpkin recipes just keeps growing and shows no sign of slowing down. 

But who agrees that there is always room for more low-carb pumpkin recipes? I thought so.

I have an entire collection of keto muffin recipes you may want to also check out.

Keto Pumpkin Cheesecake Muffins

I kept seeing these types of cheesecake-filled muffins around the web and wondered if it was something I could replicate and make keto.

What I found is that although this recipe may take a few extra steps, it is totally worth making and doable.

And in fact, that magical filling is pretty easy to add, and who knows, you may just see more of these types of muffins in the future because, let’s face it, this girl loves keto cheesecakes.

With this recipe, you are basically getting the best of a pumpkin spice muffin, a cheesecake middle, and a streusel coffee cake topping. If that’s not a winning combination, I don’t know what is.

It’s a moist, flavor-packed pumpkin muffin with a center cheesecake layer and the perfect amount of buttery crumb topping. Come on, what’s not to love?

How To Make Keto Pumpkin Cheesecake Muffins

Disclosure: Some of the links below are affiliate links, meaning at no additional cost to you, I will earn a commission if you click through and make a purchase.

Making this recipe isn’t really complicated and just takes a little more time because you will need to chill the filling since it will need to be hard enough to slice. But really that’s about it. 

So when you decide to make these keto pumpkin cream cheese-filled muffins, just give yourself enough time to allow the cheesecake filling to solidify.

In fact, you can even make the filling the day before so that you can save some time.

The reason you want to take the extra step of chilling the filling is so that it can have a better chance of staying intact while it bakes for that surprise bite of cheesecake. 

To make this recipe, you’ll need the following ingredients. Note that the full printable recipe card is at the end of the post.

You’ll need to prepare a cheesecake filling, a streusel crumb topping, and a pumpkin muffin batter. 

Then it’s just a matter of adding a layer of pumpkin muffin batter, a slice of cream cheese filling, topping with the crumb layer, and baking.

The following are all the ingredients and tools you’ll need. Please note that the full printable card is at the bottom of the page. 

Ingredients Needed To Make Pumpkin Cream Cheese Keto Muffins

Keto Pumpkin Muffin Batter

• Almond flour, finely milled
• Coconut flour
• Baking powder
• Cinnamon powder
• Pumpkin spice
• Psyllium husk powder
• Sea salt
• Ginger powder
• Unsalted butter softened
• Granulated sugar substitute
• Eggs, room temperature
• Vanilla extract
• Pumpkin puree: make sure it’s pure canned pumpkin puree and not pumpkin pie filling.

Cheesecake Filling

• Full-fat cream cheese (brick-style) softened
• Confectioner’s sugar-substitute
• Vanilla extract

Keto Streusel Topping

• Finely milled almond flour 
• Coconut flour
• Granulated sugar substitute 
• Cold butter 
• Ground cinnamon
• Pumpkin spice
• Sea salt

The Tools You’ll Need 

With only a few baking tools you can easily make these scones, the following are what I recommend. 

• Mixing bowls
• Two 12-cup capacity muffin tins
• Electric mixer
• Spatula

Sugar-Substitute Options

I have several options when it comes to which sweetener you can use in this sugar-free pumpkin cheesecake muffin recipe.

I am very partial to Lakanto Monk Fruit and I can’t help but always share this sweetener.

Lakanto Monk Fruit is my favorite because the texture and flavor are what I have found to be the closest to real sugar and because the flavor fools your taste buds like nothing else I’ve found in the market.

It’s the one sweetener that doesn’t have any aftertaste.

Having said that, I’m also partial to the brand Swerve which is an erythritol blend. Similar to Lakanto, it uses sugar alcohols and has 0% impact on blood sugar.

You could also use the stevia and erythritol-based brand Pyure if you prefer to use a stevia-based sweetener. 

Due note, that if this is your pick, make sure you reduce the amount called for in the recipe by half since it’s a much sweeter option.

Lastly, if you can’t easily find a more natural sugar substitute, you can also use Splenda with good success. I know not everyone would agree with me here, and I respect that, but in my book, it’s still better than regular sugar. 

Tag Us

I sure hope you give this low-carb pumpkin cheesecake muffins recipe a try and that once you do you will take a moment to tag us on Instagram and Facebook. It’s what keeps us encouraged to keep sharing and perfecting our recipes.

In case you don’t know, I have authored two books for you, Essential Keto Bread and Essential Keto Desserts, both inspired by your requests over the years. 

It’s my prayer these keto cookbooks will help make keto a delicious breeze for you.

Also, check out our Amazon Store for our recommendations. You might be surprised by how many great keto options are at your disposal.

Join Our Jesus And Keto Movement 

Looking for an online support system to help you stay the course on keto? As a family, we came to the keto diet looking at it from a Christian perspective. As believers, we live our lives supported by God’s grace.

So when the Holy Spirit led us to combine our Christian faith and the keto diet, we did so in hopes of finding lasting transformation.

When we followed the Holy Spirit’s prompting, we got on the path to real transformation. 

Knowing firsthand the benefits of this decision, we have created a closed Christian group that is using the keto diet to transform their lives. 

We invite you to join our private Facebook group and see if this is not the key you have been missing.

Be sure to request our FREE Jesus and Keto E-Book (First 7 Days) We hope it blesses you.

Fittoservegroup Keto App

Looking for a fast way to access our keto recipes? We got you covered. There’s an app for that. Yup, there’s a Fit To Serve Group App and it’s going to make your keto diet a delicious breeze!

Access hundreds of recipes that are all sugar-free, gluten-free, and keto-friendly.

Enjoy early access to recipes before they go live on the website. Plus, bonus recipes that are exclusive to the app. Make your own personal cookbooks that you can use to organize your favorite recipes.

Search recipes by title, ingredients, keywords, and categories, and of course, every recipe shows complete nutritional facts. 

Get the Fit to Serve Group App for easy-to-follow keto recipes made with easy-to-source ingredients. 

The app is loaded with hundreds of yummy recipes for breakfast, lunch, dinner, snacks, and even desserts!

Learn more by visiting our Fit To Serve Group App Page.