Keto Pumpkin Cream Cheese Muffins

If you are looking a delicious pumpkin recipe to celebrate fall, look no further than these keto pumpkin cream cheese muffins. Super moist pumpkin muffins swirled with cream cheese — what could be better?


keto pumpkin cream cheese muffins

It seems like every time I go to the grocery store this fall, I wind up with a can or two of pumpkin puree in my cart.  What can I say?  I’m fully embracing pumpkin spice season this year, and I’m so excited to share my latest keto pumpkin recipe: Low Carb Pumpkin Cream Cheese Muffins.

These muffins are the best of both worlds — a super moist pumpkin spice muffin base combined with a luscious cream cheese filling.  Yum!  I love them for an afternoon snack with tea, after dinner for dessert, or even — shh! — for breakfast.

Ingredients in Keto Pumpkin Muffins

To replace traditional grain flours, we’re using a mixture of almond flour and coconut flour in this recipe. I like to use an almond flour with a super-fine texture made from blanched almonds. Then, I add a bit of coconut flour. Coconut flour soaks up liquid like a sponge, so we only need to use 1/2 cup in this recipe.

You can use either canned or fresh pumpkin puree in these muffins. I like to use canned pumpkin for its convenience and consistent texture. However, if you’re up for it, you can definitely make this pumpkin bread with fresh pumpkin puree instead.



keto pumpkin cream cheese muffins

Easy Keto Pumpkin Muffin Recipe

I hope you’ll try these keto pumpkin muffins. They are scented with warm fall spices and filled with delicious pumpkin flavor.  They’re sweet, creamy, a little bit spicy, and incredibly moist.  Plus, they’re made with almond flour and coconut flour — so you know they’re low-carb and gluten-free.

Why do I love these pumpkin cream cheese muffins so much?

  • They are perfectly spiced.
  • They are super moist.
  • They are filled with a cream cheese center.
  • They keep well in the fridge.
  • They are perfect for breakfast, snack, or dessert.
  • They make a great dish for Halloween and Thanksgiving.

How to Store Pumpkin Cream Cheese Muffins

I find it’s best to store these muffins in the fridge.  And you know, I liked these muffins best served slightly chilled anyway!  But, they would also be great at room temperature if you prefer them that way.

Or, you can even freeze these pumpkin muffins. Talk about meal prep!

To do this, remove the pumpkin muffins from the pan and let them cool completely. Either wrap the muffins individually in plastic wrap, or place them in large “zip” freezer bag.

low carb pumpkin cream cheese muffins

Make Your Own Pumpkin Pie Spice

Did you run out of pumpkin pie spice?  That’s okay, you can make your own!  You only need 5 spices to make this homemade version: ground cinnamon, ground ginger, ground nutmeg, ground allspice, and ground cloves — and I bet you already have most of them in your pantry right now.

Simple DIY pumpkin spice mix (yields 1 tablespoon):

  • 1 1/2 teaspoon ground cinnamon
  • 1/2 teaspoon ground ginger
  • 1/2 teaspoon ground nutmeg
  • 1/4 teaspoon ground allspice
  • 1/4 teaspoon ground cloves

All you need to do is whisk the spices together in a small bowl, and store in an airtight container until ready to use.

pumpkin spice muffins
Aw, look at that little helper!

If you love these Pumpkin Cream Cheese Muffins, here are some other FALL recipes I know you will love:

Follow me on Instagram and tag #greenandketo so I can see all of the delicious keto treats you are making!

pumpkin spice cream cheese muffin

Keto Pumpkin Cream Cheese Muffins

Keto Pumpkin Cream Cheese Muffins

Yield: 12
Prep Time: 10 minutes
Cook Time: 20 minutes
Total Time: 30 minutes

Super moist pumpkin muffins swirled with cream cheese filling.  Keto, low-carb, and gluten-free.


  • 1/2  cup  butter softened
  • 2/3  cup  erythritol sweetener, like Swerve
  • 4  eggs large
  • 3/4  cup  pumpkin puree, see notes
  • 1  tsp  vanilla extract
  • 1 1/2  cup  almond flour
  • 1/2  cup  coconut flour
  • 4  tsp  baking powder
  • 2 tsp pumpkin spice, see notes
  • 1/2  tsp  salt
  • 8 oz cream cheese, softened


  1. Preheat the oven to 350°F. Grease a muffin pan, or line with paper muffin cups.
  2. In a large mixing bowl, cream the butter and sweetener together until light and fluffy.
  3. Add the eggs, one at a time, and mix well to combine.
  4. Add the pumpkin puree and vanilla, and mix well to combine
  5. In a separate bowl, stir together the almond flour, coconut flour, baking powder, pumpkin spice, and salt. Break up any lumps of almond flour or coconut flour.
  6. Add the dry ingredients to the wet ingredients, and stir to combine.
  7. Divide the batter into the prepared muffin tins. Add a generous tablespoon of softened cream cheese to each muffin. Use the tip of a butter knife or a toothpick to swirl the batter and the cream cheese together.
  8.  Bake for 20 - 25 minutes, or until a toothpick inserted into the center of the loaf comes out clean. (Try to test an area that is just muffin -- not cream cheese -- so you don't confuse melty cream cheese for underdone muffin batter.)


I liked these best at room temperature or slightly chilled. Store in an airtight container in the fridge.

See the post for more information about using canned vs. fresh pumpkin puree.

See the post above for a recipe for pumpkin spice mixture.



Swerve, or erythritol, is a sugar alcohol which is indigestible by humans. It has a glycemic index of 0 (meaning it does not spike blood sugar), and is, effectively, 0 net carbs.

All that to say, I count it as 0 net carbs in my calculations.

Nutrition Information:
Yield: 12
Amount Per Serving: Calories: 261 Total Fat: 23g Saturated Fat: 11g Trans Fat: 0g Unsaturated Fat: 2g Cholesterol: 99mg Sodium: 623mg Carbohydrates: 6g Fiber: 4g Sugar: 2g Protein: 7g
The nutrition information is provided as a courtesy and is approximate only. It was calculated by My Fitness Pal with the recommended brands and ingredients. All brands are different, so please verify the macros with your specific ingredients to ensure accuracy.

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keto pumpkin muffins

29 thoughts on “Keto Pumpkin Cream Cheese Muffins”

  1. Hello! I don’t see the recipe instructions!!?? I have everything measured and ready, and I just noticed that there are no instructions. Thanks!

  2. Thank you for the wonderful recipe! Is the nutrition listed somewhere I’m not looking? The recipe pasted in my carb app has them at 15 carbs per serving. I think I’m lost.

    • Hi Sue,
      Hmm, that would be a lot! Sometimes the Swerve can through off the calculators.

      My calculator put them at 260 cals, 23g fat, 7g protein, 6g carbs, and 4g fiber. So that’s 2 net carbs per muffin.

          • Swerve, or erythritol, is a sugar alcohol which is indigestible by humans. It has a glycemic index of 0 (meaning it does not spike blood sugar), and is, effectively, 0 net carbs.

            All that to say, I count it as 0 net carbs in my calculations. 🙂

        • Hi Margaret,
          Yes, depending on the specific brand of ingredients you use, the calculations could be a bit different.

          Mine came out to 260 cals, 23g fat, 7g protein, 6g carbs, and 4g fiber.

          And I edited the post to mention that the sweetener I used (Swerve) has 0 effective net carbs. Swerve, or erythritol, is a sugar alcohol which is indigestible by humans.

          Hope that helps. 🙂

          • Thank you! My thoughts are it’s like the almond flour or coconut flour that is to blame for the difference in net carbs, what brands do you use ?

  3. Sarah, I learned a trick somewhere in my years of baking that is really useful, more for cupcakes than for muffins, but both are nice. Spray the paper liners with Pam. Much fewer crumbs sticking to the papers.

  4. Trying these and just want to mention the swerve is confectioners not granulated. May be apparent to all but I was new to making w this stuff.

  5. I just made these muffins. They’re great. I’ll be making more when these are gone. These will be great for breakfast with a side of fruit. I’ll so make them adding chia seeds and pumkin seeds too.

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