Carrot Cake Muffins with Cream Cheese Filling are my definition of the perfect way to wake up. They're sweet, delicious (all while sneaking a vegetable into your breakfast), and easy to take on-the-go.

Zested carrots combine with the tender, moist crumb. Cinnamon, nutmeg, cloves, and allspice add warmth, comfort and depth of flavor. Then, a chilled vanilla cream cheese filling greets you after you take the first bite. I could eat a thousand of these.

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Looking for More Gluten Free Breakfast Baked Goods?

I also have a gluten-free carrot cake recipe that tastes very similar to these muffins and also uses zested carrots. It's one of my favorite cakes of all time.

What Makes Carrot Cake Muffins So Good?

High quality gluten-free all purpose flour containing xanthan gum. I used King Arthur's Measure for Measure.
Cinnamon. We all know and love it.
Allspice.
Nutmeg.
Cloves.
Light brown sugar. Makes these muffins have a great texture and color.
Buttermilk. Adds a little tang and tenderness. Tip: You can make your own buttermilk by adding 1 teaspoon of lemon juice or white vinegar to ⅓ cup of milk.
Pure vanilla extract. It's not a baked good without it, in my opinion.
Carrots, zested. I prefer to zest my carrots, not grate them. It completely eliminates biting into a crunchy carrot. Zested carrots combine beautifully with the crumb, which makes the muffins super moist. Zesting the carrots is a great tactic for getting children to like carrot cake as well.
Homemade cream cheese icing. I. Love. Cream. Cheese.

You could also add in other traditional carrot cake ingredients such as raisins or chopped walnuts or pecans. Keep additives limited to a total of ½ cup.

How Do I Prevent Muffins From Sticking?

I like to use a silicone muffin tray when baking anything that is muffin or cupcake shaped. It eliminates both needing to grease with butter or cooking spray and using paper or aluminum liners. This saves me time and money (since I no longer buy cooking spray or muffin liners/don't waste butter on greasing). The muffins pop out without any problem every time, no matter what recipe I use them with.

Here's the exact silicone muffin tray I use:

How to Make Carrot Cake Muffins:

Preheat the oven to 375 F. Prepare a cupcake tray by greasing it with butter or cooking spray, or use liners. Set aside.

To Make the Homemade Cream Cheese Filling: In a small-sized mixing bowl, beat the room temperature cream cheese, sugar, and pure vanilla extract together until smooth. I used an electric mixer. Set in refrigerator until ready to be used.
In a large-sized mixing bowl, whisk together the GF flour, granulated sugar, baking powder, baking soda, salt, cinnamon, allspice, cloves, and nutmeg.
In a medium-sized mixing bowl, whisk together the oil, buttermilk, eggs, vanilla, and light brown sugar until smooth.
Pour the wet ingredients into the dry and mix until just combined. It's okay to see a little bit of flour still here.
Gently fold in zested carrots and any other additives.

How to Assemble the Muffins:

Spoon about 1 ½ tbsp. of carrot cake batter into the bottom of every muffin cup.
Then, add about 2 teaspoon of cream cheese filling to the middle of every muffin.

Top the muffins with the remaining batter, about 1 tbsp. per muffin cup, covering the cream cheese filling.

Bake 20-25 minutes until golden brown and muffin tops spring back. Since altitude effects baking and ovens range in temperature output, I recommend keeping an eye on your muffins around the 15 minute mark just to see how they're looking.

Cool completely and serve.

Storage: Store these muffins in an airtight container in your refrigerator and enjoy chilled. Eat within three days.

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Gluten Free Carrot Cake Muffins with Cream Cheese Filling

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Prep Time: 20

Cook Time: 20

Cooling Time: 10

Total Time: 50

Yield: muffins

These muffins make for the perfect breakfast, snack, or dessert. Zested carrots combine with the tender, moist crumb. Cinnamon, nutmeg, cloves, and allspice add warmth, comfort and depth of flavor. Then, a chilled vanilla cream cheese filling greets you after you take the first bite.

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Equipment

Ingredients

For the Gluten Free Carrot Cake Muffins:

1 ½ cups high quality gluten-free all purpose flour containing xanthan gum I used King Arthur's Measure for Measure
½ cup light brown sugar packed
¼ cup granulated sugar
1 teaspoon baking powder
½ teaspoon baking soda
½ teaspoon salt
1 ½ teaspoon ground cinnamon
¼ teaspoon ground allspice
¼ teaspoon ground nutmeg
⅛ teaspoon ground cloves
2 large eggs room temperature
½ cup vegetable oil
⅓ cup buttermilk (make your own by adding 1 teaspoon lemon juice or white vinegar to ⅓ cup milk)
2 teaspoon pure vanilla extract
1 cup zested carrots (about 3 medium carrots) do not pack down inside the measuring cup

For the Homemade Cream Cheese Filling:

4 oz. cream cheese (½ an 8 oz. block) room temperature
⅓ cup granulated sugar
1 teaspoon pure vanilla extract

Instructions

For the Homemade Cream Cheese Icing:

In a small-sized mixing bowl, beat the room temperature cream cheese, sugar, and pure vanilla extract together until smooth. I used an electric mixer. Set in refrigerator until ready to be used.