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Keto Carrot Cheesecake Muffins

4.4 stars, average of 56 ratings

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Nothing says holidays like the smell of freshly baked carrot cake. Add a layer of vanilla-flavoured cheesecake and you end up with the perfect keto treat everyone will love, even your non-keto friends!

Looking for more recipes for the holiday season? Try some of these:

Hands-on Overall

Serving size muffin

Allergy information for Keto Carrot Cheesecake Muffins

✔  Gluten free
✔  Nightshade free
✔  Pork free
✔  Avocado free
✔  Fish free
✔  Shellfish free
✔  Beef free

Nutritional values (per serving, muffin)

Net carbs3.5 grams
Protein7.3 grams
Fat25.7 grams
Calories273 kcal
Calories from carbs 5%, protein 11%, fat 84%
Total carbs5.8 gramsFiber2.4 gramsSugars2.3 gramsSaturated fat13.7 gramsSodium269 mg(12% RDA)Magnesium30 mg(7% RDA)Potassium170 mg(8% EMR)

Ingredients (makes 9 muffins)

Cheesecake layer:
Dry muffin ingredients:
Wet muffin ingredients:
  • 4 large eggs, separated
  • 1 large egg white (use leftover egg white from the cheesecake layer)
  • 1/3 cup + 1 tbsp virgin coconut oil or butter, melted (90 g/ 3.2 oz)
  • 3/4 cup finely grated carrots (83 g/ 2.9 oz)
  • 20-30 drops liquid Stevia extract (NuNaturals or SweetLeaf)
  • melted coconut oil or ghee for greasing


  1. Preheat the oven to 160 °C/ 320 °F. Line a muffin tray with 9 medium muffin paper cups. Grease each cup with a small amount of coconut oil or ghee. Prepare the cheesecake layer by whisking the cream cheese, egg yolk, powdered Erythritol and vanilla powder. Set aside. Keto Carrot Cheesecake Muffins
  2. Place all the dry muffin ingredients - apart from the pecans - into a bowl and combine well.
    I make my own chia seed meal by blending it in a food processor for just a few seconds until powdered. Keto Carrot Cheesecake Muffins
  3. Finely grate the carrot and roughly chop the pecans. Set aside. Keto Carrot Cheesecake Muffins
  4. Separate the egg whites from the egg yolks. In a bowl, using a hand beater or electric mixer), whip up the four egg whites until they create soft peaks.
    Place the four egg yolks into a bowl and add the leftover egg white from the cheesecake layer. Add melted coconut oil, stevia and process until smooth (the coconut oil should be melted and cooled, don't use hot oil). Process until well combined and start adding the dry mixture - a tablespoon or two at a time while mixing. Keto Carrot Cheesecake Muffins
  5. Add a quarter of the whipped egg whites and mix gently. Add the remaining egg whites and fold in the batter using the slow setting on your mixer or using a spatula. Keto Carrot Cheesecake Muffins
  6. Be careful not to deflate the egg whites and keep the batter as fluffy as you can. Add the carrot and pecans and slowly fold in. Keto Carrot Cheesecake Muffins
  7. Spoon the batter into the paper cups and using a small spoon, create small wells in the centre of the muffing mixture. Keto Carrot Cheesecake Muffins
  8. Fill each muffin with a heaping tablespoon of the reserved cheesecake mixture (about an ounce / 30 grams per muffin). Transfer into the oven and bake for 30-35 minutes or until the tops are set and golden brown. Keto Carrot Cheesecake Muffins
  9. When done, remove from the oven and place on a cooling rack. Then, place in an airtight container and keep in the fridge for up to 3 days, or store in the freezer for up to 3 months. Enjoy! Keto Carrot Cheesecake Muffins

Ingredient nutritional breakdown (per serving, muffin)

Net carbsProteinFatCalories
Cream cheese, soft (full-fat)
0.6 g1.4 g5.6 g49 kcal
Egg yolk, fresh
0.1 g0.3 g0.5 g6 kcal
Erythritol (natural low-carb sweetener)
0.1 g0 g0 g0 kcal
Vanilla extract, powder (vanilla bean)
0 g0 g0 g0 kcal
Almond flour (blanched ground almonds, almond meal)
0.5 g1.2 g2.9 g33 kcal
Coconut flour, organic
0.3 g0.5 g0.4 g10 kcal
Chia seed meal (ground chia seeds)
0 g0.2 g0.3 g5 kcal
Erythritol (natural low-carb sweetener)
0.3 g0 g0 g1 kcal
Baking powder, gluten-free
0.2 g0 g0 g1 kcal
Cinnamon, spices
0.1 g0 g0 g1 kcal
Vanilla extract, powder (vanilla bean)
0.1 g0 g0 g1 kcal
Spices, ginger, ground
0.1 g0 g0 g1 kcal
Allspice, dried, spices
0 g0 g0 g0 kcal
Nutmeg, spices
0 g0 g0 g0 kcal
Salt, pink Himalayan rock salt
0 g0 g0 g0 kcal
Pecans, nuts
0.2 g0.5 g4 g38 kcal
Egg, whole, fresh, raw (free-range or organic eggs)
0.2 g2.8 g2.1 g32 kcal
Egg white, fresh
0 g0.4 g0 g2 kcal
Coconut oil, extra virgin
0 g0 g9.9 g89 kcal
Carrot, fresh
0.6 g0.1 g0 g4 kcal
Stevia extract (SweetLeaf or NuNaturals, natural low-carb sweetener)
0 g0 g0 g0 kcal
Total per serving, muffin
3.5 g7.3 g25.7 g273 kcal

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Martina Slajerova
Creator of

Martina Slajerova

I changed the way I ate in 2011, when I was diagnosed with Hashimoto’s, an autoimmune disease that affects the thyroid. I had no energy, and I found it more and more difficult to maintain a healthy weight.

That’s when I decided to quit sugar, grains, and processed foods, and to start following a whole-foods-based ketogenic approach to food.

Let us know what you think, rate this recipe!

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Comments (17)

I loved this recipe, similar flavours to carrot cake with cream cheese frosting. Yummy! It was a bit labour intensive and used up a ton of bowls and counter space, but worth the effort. Thanks for sharing.

Thank you Kathleen!

Made this for our Thanksgiving dessert, and it was very good.  There was quite a bit of prep, so will probably default to the cinnamon mug cake in the future (which is also very good and only takes a few minutes to make) 😀

Thank you for your lovely feedback!

I made this recipe and LOVED it!  However, I'm wondering if it might be possible to boost the protein a bit by adding protein powder to the recipe. Any ideas on how to do that?
Oh, I also snapped a great picture (IMO). I added some shredded carrot and a pecan half to the top of the muffin.  They look great and taste even better!

Thank you for your kind words Ann! Yes, you could use an additional 1/4 cup protein powder, plus you will need to use about 1/4 cup almond milk. The additional protein powder will also help the muffins rise. I think the photo may be private because it doesn't seem to be working?

Thanks for the info. I'm going to make them again with the protein powder!  
Sorry about the photo link.  I posted it to Facebook. It's probably because we're not connected as friends.  
Here's a link to the photo on Box:
Feel free to use it. I thought it turned out nicely for a snap taken on my iPhone. 😊

Thank you Ana, they look fantastic! I think that at some point we should enable photo uploads so that people can share their creations 😊

These are amazing! I tweaked them a little and used the pumpkin cheesecake topping from your cheese bread. We have two picky eaters in our family and they both really like them. Thank you!

Thank you Emily, that sounds great, I need to try them with the pumpkin/orange  topping! 😊

Hi Martina,
can you make me an example of a 'full-fat cream cheese', I don't know which one to use.
Thanks a lot

Hi Simona, I used Philadelphia cream cheese (the "Original" one with 21.5 g fat per 100 g).


This looks fantastic!  I don't have carrots, but I do have pumpkin and I am going to put this great sounding topping on your Pumpkin Chia Muffins!!!!

Sounds perfect to me! Let me know how they turned out 😊

These turned out great!  The spices went well with the cream cheese topping!  This is going to be one of my go-to  recipes!   Now for your next about a banana walnut muffin?!

Thank you Jill! I love those flavours but I don't cook with bananas (not for keto)... banana extract may work though 😊