Coconut Free/ Desserts/ Gluten Free/ Low Carb/ Thanksgiving Recipes/ Vegetarian

Pumpkin Muffins with Cream Cheese Filling

pumpkin cream cheese muffins

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Pumpkin muffins with a cream cheese filling is a delicious muffin with a yummy centre.  Baked with almond flour these muffins are low carb & gluten free.

Just as I was about to spoon the muffin mixture into the tin, I was thinking about the cream cheese frosting and thought, why not put the topping inside the muffin?  So whipped up some cream cheese, and voila!  Luckily for me it worked out, despite my fear of the filling oozing out during baking.   

pumpkin muffin cream cheese filling

Keto Cream Cheese Muffins

Cream cheese seems to go so well with a spicy pumpkin’s almost a classic flavour combination.   I tried to keep the sweetness down as I find pumpkin sweet enough, and the cream cheese filling adds to this.  However, if you prefer a sweeter muffin, double up the erythritol.

These pumpkin muffins are moist and packed full of flavour thanks to the spices. The creamy cream cheese centre is not too sweet but adds an extra delight to the muffins.

I love using pumpkin as well as being low in carbs, it has a lovely bright colour.  Almost cheerful in it’s appearance which you need during Fall as the winter nights are soon to descend upon you. Well, that’s for you living in the Northern Hemisphere. I’ll try to refrain from posting my beach photos in November!

pumpkin muffin with cream cheese centre

How To Make Pumpkin Keto Cream Cheese Muffins

The pumpkin spice gives the muffin sponge a delicious warm flavour. If you don’t have ready made pumpkin spice you can easily make your own. In a jar, mix 3 tablespoons cinnamon, 2 teaspoons ground ginger, 2 teaspoons nutmeg, 1 teaspoon all spice and 1 teaspoon ground cloves. Shake and mix and store for pumpkin baking.

For the sweetener in both the muffin and the cream cheese centre I used erythritol. There is also a blend of Monk Fruit with erythritol I enjoy when I can get my hands on a packet. Since I have dogs, I now never use Xylitol as it’s deadly for dogs if they consume it. Nothing is safe in my kitchen if I turn my back or drop a muffin, so it’s a big no now. I happily used it before so if you have an animal free household, that can be used.


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pumpkin cream cheese muffins

Pumpkin Muffins with Cream Cheese Filling

Low carb pumpkin muffins baked with almond flour and a cream cheese filling
4.16 from 33 votes
Print Pin Rate
Servings: 9 Muffins
Calories: 162kcal
Author: Angela Coleby


  • 2 cups Almond Flour
  • 2 teaspoon baking powder
  • 1/4 cup Butter, unsaled melted
  • 4 Eggs
  • 1/2 cup Pumpkin puree
  • 1/4 cup water
  • 1 teaspoon Pumpkin spice
  • 1/2 teaspoon Salt
  • 1/4 cup Erythritol or sweetener


  • 3 oz Cream cheese softened
  • 2 tablespoons Erythritol or sweetener
  • 1 teaspoon vanilla extract


  • Preheat the oven to 180C/350F degrees.
  • Mix the dry ingredients in a bowl.
  • In another bowl, blend the pumpkin and eggs (I used a whisk) until thoroughly blended.
  • Add the butter and continue to blend.
  • Combine the dry ingredients with the pumpkin mixture, add the water and mix well.
  • Mix the filling ingredients together until smooth and blended.
  • Lin a muffin tin with paper cases.
  • Spoon the pumpkin mixture into the cups about 2/3 of the way up.
  • Make a “well” in the mixture. I used a small spoon to do this, pushing the mixture around the sides.
  • Place about a teaspoon of the cream cheese filling into your “well” in the muffin mixture.
  • Cover the centre with the rest of the muffin mixture, smoothing it over if required.
  • Bake for 25 -30 minutes, until the top of the muffin is firm.
  • Eat and enjoy!


The net carbs will be the total carb count minus the fibre count. Carb count excludes sugar alcohols.
Any nutritional analysis on the website is based on an estimate, calculated by from the individual ingredients in each recipe. Variations may occur for various reasons, including product availability and food preparation. We make no representation or warranty of the accuracy of this information.


Serving: 1muffin | Calories: 162kcal | Carbohydrates: 3g | Protein: 5g | Fat: 15g | Fiber: 1g
Tried this recipe?Mention @Divalicious_Recipes or tag #divaliciousrecipes
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  • Reply
    October 4, 2019 at 5:26 pm

    We can get pumpkin puree here but have not seen pumpkin spice. Can you give ingredients to mix it up please?

    • Reply
      Angela Coleby
      October 8, 2019 at 9:53 am

      3 tablespoons ground cinnamon
      2 teaspoons ground ginger
      2 teaspoons ground nutmeg
      1 teaspoon ground allspice
      1 teaspoon ground cloves

  • Reply
    Tracy Mills
    September 27, 2019 at 3:16 pm

    I was missing muffins a lot, and these are delish!! Thanks so much for this recipe!!

    • Reply
      Angela Coleby
      September 28, 2019 at 8:08 am

      Thank you! Glad you enjoyed them.

  • Reply
    November 22, 2018 at 5:11 pm

    Tried these a couple days ago. The first day, they were amazing. The second and third day, they are now really dry. Any thoughts?

    • Reply
      Angela Coleby
      November 24, 2018 at 10:54 am

      Did you store them in a container?

  • Reply
    Christy Sharp
    November 6, 2018 at 12:23 pm

    Can I bake this in a bread pan instead?

    • Reply
      Angela Coleby
      November 8, 2018 at 10:10 pm

      Great idea and cannot see why not! Perhaps a longer baking time though.

  • Reply
    October 31, 2018 at 2:27 am

    These muffins are my absolutel favorite! I make a batch every week!

  • Reply
    October 29, 2018 at 4:38 am

    These were absolutely delicious. Thank you.

    • Reply
      Angela Coleby
      October 30, 2018 at 7:45 am

      Thanks! Glad you enjoyed them!

  • Reply
    October 20, 2018 at 1:34 pm

    What spice combo can I use to make the pumpkin pie spice? Thanks!

  • Reply
    Kearney Terhune
    September 29, 2018 at 9:38 pm

    Made these today… can I say you TOTALLY rocked my world!!! I LOVE pumpkin spice ANYTHING and these are AMAZING! I used Monk fruit sweetener and still yummy as ever!

    • Reply
      Angela Coleby
      October 1, 2018 at 11:33 am

      Glad you enjoyed them!

    • Reply
      October 8, 2018 at 12:05 pm

      I used foil lined muffin tin liners and they stuck a bit anyone else have this issue?

  • Reply
    September 27, 2018 at 7:11 pm

    These look so god!! Would it be ok to use Swerve as a sweetener? Would it be the same amount?

    • Reply
      Angela Coleby
      September 29, 2018 at 10:06 am

      Yes, the amount should be the same, but taste test as you go along!

      • Reply
        Kristy Fountain / @thiswildway
        November 20, 2018 at 1:41 am

        I used Swerve, and they didn’t seem sweet enough to me. They turned out more like pumpkin rolls with that amount of Swerve (either that or my measurement was off). Next time I’ll add more! Hope that helps.

        • Reply
          Angela Coleby
          November 20, 2018 at 12:25 pm

          Different sweetener can often yield different results. As does coconut flour.

  • Reply
    October 23, 2017 at 2:03 pm

    Angela, this is one of those recipes that stand out in the crowd! There are so many muffins out there but these are unbelievable! The topping is so nice and inviting that it is hard NOT to try it. I would love to make these some day because you’ve done a great job and made it clear that muffins can be surprising!

    • Reply
      Angela Coleby
      October 23, 2017 at 5:54 pm

      Thank you! Check out my savoury muffins for something different too!

  • Reply
    November 1, 2013 at 3:31 pm

    Hi – can I substitute another sweetener like maple syrup or honey?

    • Reply
      November 3, 2013 at 10:56 am

      Hi Amy, yes you can. As the pumpkin puree is very moist, I would not add too much as you may be left with a soggy muffin. Good luck and let me know how it works out!

  • Reply
    October 20, 2013 at 8:51 pm

    Will be trying these! Great recipe!

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