Start your morning off on the right foot with these irresistible Carrot Cake Muffins with cream cheese filling! Moist and flavorful muffins packed with grated carrots, spices and a surprise filling of creamy, tangy cream cheese.

carrot cake muffins arranged around carrots, a spoon of spices, and one muffin broken open to reveal the cream cheese filling inside

If you love carrot cake with cream cheese frosting, you will be obsessed with these carrot cake muffins. You don’t have to wait for a special occasion, these are an afternoon snack with a cup of coffee type of muffin. You could even keep these on hand for an easy breakfast option!

Some people don’t love the idea of shredded carrot and cake together, but you’re missing out if you don’t try this carrot muffin recipe!

Warm spices, fresh carrots, and creamy filling come together in the perfect way in this carrot cake muffins recipe. You’re going to want to make a double batch, don’t say I didn’t warn you!

Why You’ll Love These Carrot Cake Muffins

  • Super soft and moist muffins
  • Cream cheese filling inside
  • Made with everyday ingredients
  • Great way to use up carrots!
a pile of carrot cake muffins sitting on a white cake platter with carrots beneath it and one of the muffins half eaten, revealing the cream cheese filing inside

What You’ll Need for these Carrot Muffins

This delicious carrot cake muffin recipe is made with mostly everyday ingredients that you likely already have in your kitchen. Get the full measurements in the recipe card below.

  • All-purpose flour – measured by using the spoon and level method or by weight on a food scale
  • Granulated sugar
  • Brown sugar
  • Baking powder
  • Salt
  • Ground cinnamon
  • Ground ginger
  • Ground nutmeg
  • Ground cloves
  • Large eggs
  • Buttermilk
  • Vegetable oil
  • Vanilla extract
  • Grated carrots
  • Cream cheese – Don’t forget to let it soften!
a pile of carrot cake muffins and carrots, with the muffin on top bitten into, revealing the cream cheese filling inside

How to Make Carrot Cake Muffins with Cream Cheese Filling

Your whole family is going to love these carrot muffins! Get the full recipe in the recipe card below.

Carrot Cake Muffins

Grate carrots. Using a box grater or cheese grater, grate the carrots and measure 2 cups.

Mix dry ingredients. In a large mixing bowl combine the flour, cup of sugar, brown sugar, baking powder, salt, cinnamon, ginger, nutmeg and cloves. Stir with a spoon to combine and set aside.

Mix wet ingredients. In a separate bowl combine the eggs, buttermilk, vegetable oil, and vanilla extract. Stir to combine with a spatula or beat with an electric mixer on low for 30 seconds.

Combine all ingredients. Gradually mix in the dry ingredients, mixing just until combined. Using a spatula, gently fold in the grated carrots. The batter will be very thick!

batter for carrot cake muffins in a clear glass mixing bowl

Rest batter. Cover the bowl with a towel and allow the batter to rest for 15 minutes. During this time, preheat the oven to 425ºF and prep the cream cheese layer.

Cream Cheese Layer

Beat cream cheese. Place the room temperature cream cheese in a mixing bowl and beat with an electric mixer for 1-2 minutes, until smooth.

Make cream cheese mixture. Add in the sugar and vanilla extract, and beat until combined.

Assemble

Fill muffin liners. After the 15 minute rest, fill the paper liners ½ full with batter, then add 1-2 tablespoons of the cream cheese mixture, then top each muffin with more batter, all the way to the top. The muffin cups should be very full!

Top with sugar. Sprinkle the muffins with sanding sugar.

Bake and cool. Bake for 9 minutes at 425ºF, then keep the muffins in the preheated oven, and turn the temperature down to 350ºF and bake for 10-13 minutes or until a toothpick inserted in the center comes out clean. Allow the muffins to cool in the pan for 15 minutes before removing.

Tips for the Best Carrot Cake Muffins

Properly measure the flour. Measure the flour using the spoon and level method or by weight using a food scale.

Baking powder is key. Use baking powder, do not swap for baking soda.

Stick with buttermilk. For best results, make these carrot muffins with buttermilk. This recipe has not been tested with whole milk, skim milk, or a milk alternative.

Be sure to rest the batter. Allow the batter to rest for 15 minutes.

Bake at high temp first. Bake at a higher temperature initially to cause the muffins to rise quickly. Read more tips to make a bakery-style muffin top below.

How to Create Bakery Style Muffin Tops

Bakery style muffins are known for their domed tops. Plus who doesn’t love them? I used a few techniques to help “lift” these muffins so they would have domed tops.

1. THE REST PERIOD

Let the batter rest for 15 minutes after it’s mixed and before you scoop it into the muffin pan. During the resting period, starch molecules in the flour are absorbing the liquid in the batter, causing them to swell and giving the batter a thicker consistency (ref the kitchen whisper). Our 15 minute rest is just a quick rest.

2. BAKE AT HIGH TEMPERATURE INITIALLY

Bake the muffins at a high temperature (425ºF) for 9 minutes then lower to 350ºF. Starting the muffins off at a higher temperature causes the batter to rise rapidly, producing a domed shape.

3. FILL THEM TO THE TOP

Fill your muffin liners to the top with batter. Yes, this goes against everything you’re heard but it’s important in helping the muffin gain that height.

carrot cake muffins arranged around carrots, a spoon of spices, and one muffin broken open to reveal the cream cheese filling inside

Substitutions & Variations

  • Gluten Free Carrot Cake Muffins. I’ve made these muffins with both regular and gluten-free flour with awesome results on multiple occasions. I recommend King Arthur’s Gluten Free Measure for Measure Flour. Use it as a one-for-one substitute for regular flour.
  • Add nuts. Carrot cake pairs well with nuts. Add in 1/2 cup chopped pecans or walnuts!

FAQs

Can I freeze carrot cake muffins?

Yes, these carrot muffins freeze well. You’ll want to wrap them individually in plastic wrap. You can also wrap two together, with the bottoms of the muffin liner touching, if you’ll want to pull two from the freezer at a time. Wrap them tightly in plastic wrap, then place them in an airtight container or freezer-safe bag. Thaw on the counter to room temperature or pop them in the microwave for 15-second intervals until warmed.

How long do carrot cake muffins with cream cheese filling last?

These carrot cake muffins can be stored in the refrigerator for about 4-5 days in an airtight container.

More Muffin Recipes

Carrot Cake Muffins

5 from 1 rating
Prep Time: 15 mins
Cook Time: 30 mins
Resting Time: 15 mins
Total Time: 1 hr
Yield: 15 muffins
Start your morning off on the right foot with these irresistible Carrot Cake Muffins with cream cheese filling! Moist and flavorful muffins packed with grated carrots, spices and a surprise filling of creamy, tangy cream cheese.

Ingredients

Muffins

  • 2 ½ cups all purpose flour, 300 grams
  • 1 cup granulated sugar
  • ½ cup brown sugar
  • 2 tsp baking powder
  • ½ tsp salt
  • 1 ½ tsp ground cinnamon
  • ¼ tsp ground ginger
  • ¼ tsp ground nutmeg
  • tsp ground cloves
  • 2 large eggs
  • ¾ cup buttermilk
  • ½ cup vegetable oil
  • 1 tsp vanilla extract
  • 2 cups grated carrots

Cream Cheese Layer

  • 8 oz cream cheese, room temperature
  • ½ cup granulated sugar
  • 2 tsp vanilla extract

Instructions
 

Muffins

  • Using a box grater or cheese grater, grate the carrots and measure 2 cups.
  • In a mixing bowl combine the flour, granulated sugar, brown sugar, baking powder, salt, cinnamon, ginger, nutmeg and cloves. Stir with a spoon to combine and set aside.
  • In a larger mixing bowl combine the eggs, buttermilk, vegetable oil, and vanilla extract. Stir to combine with a spatula or beat with an electric mixer on low for 30 seconds.
  • Gradually mix in the dry ingredients, mixing just until combined. Using a spatula, gently fold in the grated carrots. The batter will be very thick!
  • Cover the bowl with a towel and allow the batter to rest for 15 minutes. During this time, preheat the oven to 425ºF and prep the cream cheese layer.

Cream Cheese Layer

  • Place the room temperature cream cheese in a mixing bowl and beat with an electric mixer for 1-2 minutes, until smooth. Add in the sugar and vanilla extract, beat until combined.

Assemble

  • After the 15 minute rest, fill the liners ½ full with batter, then add 1-2 tablespoons of the cream cheese mixture, then top each muffin with more batter, all the way to the top. The muffin cups should be very full!
  • Sprinkle the muffins with sanding sugar.
  • Bake for 9 minutes at 425ºF, then keep the muffins in the oven, and turn the temperature down to 350ºF and bake for 10-13 minutes or until a toothpick inserted in the center comes out clean. Allow the muffins to cool in the pan for 15 minutes before removing.

Notes

  • Measure the flour using the spoon and level method or weigh it on a scale.
  • I’ve made these muffins with both regular and gluten free flour with awesome results on multiple occasions. I recommend King Arthur’s Gluten Free Measure for Measure Flour. Use it as a one for one substitute for regular flour.
Cuisine: American
Course: Dessert
Author: Beth
Calories: 335kcal, Carbohydrates: 47g, Protein: 5g, Fat: 14g, Saturated Fat: 5g, Polyunsaturated Fat: 5g, Monounsaturated Fat: 3g, Trans Fat: 0.1g, Cholesterol: 41mg, Sodium: 218mg, Potassium: 142mg, Fiber: 2g, Sugar: 30g, Vitamin A: 3113IU, Vitamin C: 1mg, Calcium: 84mg, Iron: 1mg
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