Gluten-Free Carrot Cheesecake Muffins

Prep: 35 minCook: 10 min9 muffinsmediumAmerican
Carrot Cheesecake Muffins with Almond Flour and Pecans

These fluffy carrot muffins feature a rich cream cheese center and warm spices like cinnamon and ginger. Made with almond flour and coconut flour, they're naturally low in carbs and perfect for breakfast or dessert. The technique of whipping egg whites separately creates an incredibly light texture, while grated carrots and chopped pecans add natural sweetness and crunch. Each muffin gets a generous dollop of vanilla cheesecake filling that creates a delightful surprise in every bite.

Ingredients

Yield: 9 muffins
  • ¾ cup full-fat cream cheese
  • 1 large egg yolk, reserve egg white for the muffin
  • 2 tbsp Erythritol or Swerve, powdered
    monk fruit sweetener1:1keto

    slightly different sweetness level

    Full guide →
  • ¼ tsp vanilla bean powder or 1 tsp unsweetened vanilla extract
  • ½ cup almond flour
    coconut flour1:4 ratiopaleo

    will be denser

    Full guide →
  • 2 heaping tbsp coconut flour
  • 1 tbsp ground chia seeds
  • ¼ cup granulated Erythritol, Swerve or Sukrin Gold
    monk fruit sweetener1:1keto

    slightly different sweetness level

    Full guide →
  • 2 tsp gluten-free baking powder
  • 1 tsp cinnamon
  • 1 tsp vanilla powder
  • 1 tsp ground ginger
  • tsp ground allspice
  • tsp nutmeg
  • tsp salt
  • ½ cup pecans, roughly chopped
    walnuts1:1none

    different flavor profile

    Full guide →
  • 4 large eggs, separated
  • 1 large egg white, use leftover egg white from the cheesecake layer
  • cup + 1 tbsp virgin coconut oil or butter, melted
    butter1:1dairyadds dairy

    richer flavor

    Full guide →
  • ¾ cup carrots, finely grated
  • 20 drops liquid Stevia extract
  • melted coconut oil or ghee, for greasing
    butter1:1dairyadds dairy

    richer flavor

    Full guide →

Instructions

  1. 1

    Preheat the oven to 325°F

  2. 2

    Line a muffin tray with 9 medium muffin paper cups and grease each cup with coconut oil or ghee

  3. 3

    Prepare the cheesecake layer by whisking the cream cheese, egg yolk, powdered erythritol and vanilla powder, then set aside

  4. 4

    Place all the dry muffin ingredients except pecans into a bowl and combine well

  5. 5

    Finely grate the carrot and roughly chop the pecans, then set aside

  6. 6

    Separate the egg whites from the egg yolks

  7. 7

    Whip the four egg whites until they create soft peaks

  8. 8

    Place the four egg yolks into a bowl and add the leftover egg white from the cheesecake layer

  9. 9

    Add melted and cooled coconut oil and stevia to the yolk mixture and process until smooth

  10. 10

    Add the dry mixture a tablespoon or two at a time while mixing

  11. 11

    Add a quarter of the whipped egg whites and mix gently

  12. 12

    Fold in the remaining egg whites carefully to keep the batter fluffy

  13. 13

    Add the carrot and pecans and slowly fold in

  14. 14

    Spoon the batter into the paper cups and create small wells in the center of each muffin

  15. 15

    Fill each well with a heaping tablespoon of the cheesecake mixture

  16. 16

    Bake for 30-35 minutes or until the tops are set and golden brown

  17. 17

    Remove from oven and place on a cooling rack

Tips

Tip 1

Make your own chia seed meal by blending whole chia seeds in a food processor for just a few seconds until powdered.

Tip 2

Ensure the coconut oil is melted and cooled before adding to prevent cooking the eggs.

Tip 3

Be gentle when folding in egg whites to maintain the fluffy texture that makes these muffins light.

Good to Know

Storage

Keep in an airtight container in the fridge for up to 3 days, or store in the freezer for up to 3 months.

Make Ahead

Can be made 1-2 days ahead and stored covered in the refrigerator.

Serve With

Serve at room temperature or slightly warmed.

Common Mistakes

Watch

Don't use hot melted coconut oil as it will cook the eggs.

Watch

Avoid overmixing when folding in egg whites to maintain fluffiness.

Watch

Don't skip greasing the muffin cups even with paper liners to prevent sticking.

Substitutions

Dairy-Free Swaps

Coconut oil
butter1:1dairyadds dairy

richer flavor

Full guide →

General Alternatives

Erythritol
monk fruit sweetener1:1keto

slightly different sweetness level

Full guide →
Pecans
walnuts1:1none

different flavor profile

Full guide →
Almond flour
coconut flour1:4 ratiopaleo

will be denser

Full guide →
Find more substitutions →

FAQ

Can I make these without the cheesecake layer?

Yes, you can omit the cheesecake filling and just make carrot muffins. Reduce baking time to 20-25 minutes and check for doneness with a toothpick.

What if I don't have liquid stevia?

You can substitute with additional powdered erythritol, using about 2 tablespoons more, though the sweetness level may vary slightly.

How long do these keep frozen?

These muffins freeze well for up to 3 months. Thaw overnight in the refrigerator or at room temperature for 2-3 hours before serving.