Home » desserts » (Ultra Tender!) Keto Pumpkin Cream Cheese Muffins 🎃

(Ultra Tender!) Keto Pumpkin Cream Cheese Muffins 🎃

Ultra tender, incredibly moist and beautifully spiced– these keto pumpkin cream cheese muffins are a total dream… at just 3g net carbs!

Keto pumpkin cream cheese muffins on a baking tray with pumpkin seeds

Keto Pumpkin Cream Cheese Muffins

A Starbucks Copycat!

A spinoff of my famous keto pumpkin bread, these guys incorporate a luscious cheesecake filling to give them a little extra oomph (Starbucks style!).

And these aren’t your average dense and eggy keto muffins either- they’re light, tender and extra fluffy (yup, even when baked with a filling!).

The filling

The cream cheese filling for these pumpkin muffins is simply a cheesecake-like batter consisting of cream cheese, an egg yolk and a little sweetener.

But, and this is a big but, I also must say that I thoroughly enjoyed these guys too by simply popping in a dollop of just cream cheese in the center. Different for sure (think a little more savory), but I know this is an idea that might appeal to some of you who are also trying to keep sweeteners at a minimum.

Overhead shot of the cream cheese filling with an egg yolk and sweetener Unbaked keto pumpkin cream cheese muffins on a tray with paper liners

The Sweetener

You’ve got good options here! Allulose is my favorite for best texture and no aftertaste now (you do need to add 30% more though), Lakanto Golden (baked goods with erythritol can have a slight hard texture, still not big deal here though), xylitol (non-corn though to avoid tummy troubles!).

Pyure (an erythritol and stevia blend) is also a good one for muffins and quick breads, particularly if you’re trying to limit your sugar alcohol consumption (it’s added stevia makes it twice as sweet as sugar… i.e. you add half!).

Oh, and if not restricted by sugars, simply sub 1-to-1 with coconut or regular sugar.

And if using xylitol, make sure to be careful if you have a pup (or kitty!) around the house, as it’s highly toxic to the little guys! 🐕

The Flours

I like a mixture of super fine almond flour, psyllium huskcoconut flour and golden flaxseed meal best (click through for the specific brands I use). Oh, and no xanthan gum is needed here to yield a wonderful and moist crumb (hurray!)

Just keep in mind that for best texture and rise, you’ll always want to regrind your flaxseed meal in a dry blender or bullet. And be sure you’re either using either very finely ground psyllium powder or to regrind your husks!

Closeup of keto pumpkin muffins filled with cheesecake and garnished with pumpkin seeds

Keto pumpkin cream cheese muffins on a baking tray with pumpkin seeds

Keto Pumpkin Cream Cheese Muffins 🎃

Ultra tender, incredibly moist and beautifully spiced- these keto pumpkin cream cheese muffins are a total dream... at just 3g net carbs!
5 from 3 votes
Prep Time 30 minutes
Cook Time 30 minutes
Total Time 1 hour
Course Breakfast, Dessert
Cuisine American
Servings 12 muffins
Calories 177 kcal


For the cream cheese filling

For the pumpkin muffins


  • Make the cream cheese filling by beating the cream cheese with an electric mixer until soft and creamy. Add in the sweetener, egg yolk, vanilla and salt and mix until smooth. Set aside while you prepare the rest.
  • Preheat oven to 350°F/180°C and line a muffin pan.
  • Whisk together in a medium bowl almond flour, coconut flour, golden flaxseed meal, psyllium husk, pumpkin pie spice, baking powder and salt. Set aside. 
  • Beat the eggs with the sweetener until light and fluffy (about 3 minutes). Mix in the vinegar, butter and pumpkin puree.
  • Add in the dry flour mixture and mix everything is super thoroughly incorporated.
  • Distribute batter evenly into muffin pan, smoothing out the top with wet fingertips. Drop a tablespoon of the cheesecake filling (or a little square of cream cheese itself) and bake for 28-32 minutes, until deep golden and a toothpick inserted comes out clean. Check in after minute 15, and cover with aluminum foil as soon as it begins to turn golden (about minute 20 for me). 
  • Allow to cool for 15 minutes in the pan before removing, and cool completely on a rack. Store in an airtight container in the fridge for 3 days and freeze for up to 3 months.


*For best texture and rise, always regrind your psyllium husk (or powder) and flax meal in a dry blender or bullet. 


Serving: 1muffin | Calories: 177kcal | Carbohydrates: 7g | Protein: 5g | Fat: 13g | Saturated Fat: 4g | Cholesterol: 69mg | Sodium: 174mg | Potassium: 76mg | Fiber: 4g | Sugar: 1g | Vitamin A: 3105IU | Vitamin C: 0.7mg | Calcium: 48mg | Iron: 1.1mg
Keyword almond flour pumpkin cream cheese muffins, keto pumpkin cheesecake muffins, keto pumpkin cream cheese muffins
Whip up this recipe?Comment below or drop me a line @gnomgnom._ and tag #gnomgnomyum!


  1. Sio says:

    5 stars
    Love em! Suuuuuper great with a cuppa and some eggs.

    TIP you have about half a can of pumpkin left over. Plan accordingly! I wish I’d picked up ingredients to make the pumpkin cheesecake ice cream! Oh well! I slid my bonus pumpkin into some curry and all is well.

  2. Jinna says:

    5 stars
    You did it again!! Another solid, easy, and delicious recipe!!! These muffins are super soft, fluffy, and delicious and the cream cheese filling is where it is at!! 😋🙌🏻

  3. Shannon says:

    5 stars
    Yum! I made these last night and they are the best keto muffins I’ve ever made. I used the recipe as written, only adding about 1/2 cup chopped pecans to the batter. The texture is excellent! Thank you for your reliable recipes!

    • Paola van der Hulst says:

      Oh Shannon adding pecans sounds like an awesome idea, can’t wait to try! Thanks for reporting back, its my absolute pleasure 😉

    • Paola van der Hulst says:

      Yes Lisa! I wrote a little note on that right next to it, that you can sub with more golden flaxseed (but I also suggest adding a little xanthan gum then to make up for the loss in binding agent). Xo.

  4. Luci says:

    I’m allergic to coconut. What’s the best sub for the coconut flour and coconut cream? This recipe sounds amazing and definitely want to try this weekend.

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