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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.

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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 this Carrot Cake Muffin Recipe

  • Super soft and moist muffins
  • Cream cheese filling inside
  • Made with everyday ingredients
  • Great way to use up carrots!
carrot cake muffin with bite removed to show cream cheese filling

Ingredients for Carrot Cake 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!

How to Properly Measure Flour

The most accurate way to measure flour is to use a kitchen scale, weighing it in grams. 

If you don’t have a kitchen scale, follow this method. 

  • Aerate the flour with a whisk or spoon. Flour becomes heavy and compact as it sits. Aerating is the same as fluffing the flour, but not the same as sifting it. Do not sift the flour unless the recipe specifically calls for it.
  • Use a spoon to sprinkle the flour into the measuring cup. Do not tap the cup against the counter, as this will compact the flour.
  • Use the back of a butter knife to level off the excess.
carrot cake muffins arranged around carrots, a spoon of spices, and one muffin broken open to reveal 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

  1. Grate carrots. Using a box grater or cheese grater, grate the carrots and measure 2 cups.
  2. 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.
  3. 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.
  4. 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!
  5. 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.
batter for carrot cake muffins in a clear glass mixing bowl

Cream Cheese Layer

  1. 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.
  2. Make cream cheese mixture. Add in the sugar and vanilla extract, and beat until combined. Put the bowl of cream cheese filling in the freezer while you prep the rest of the recipe.

Assemble

  1. Fill muffin liners. After the 15 minute rest, fill the paper liners with ONLY 1-2 tablespoons of 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!
  1. Top with sugar. Sprinkle the muffins with sanding sugar.
  2. Bake and cool. Bake for 7 minutes at 425ºF, then keep the muffins in the preheated oven, and turn the temperature down to 350ºF and bake for 12-15 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.

Carrot Cake Muffins Recipe Tips

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.

4. Bonus Tip – FILL EVERY OTHER MUFFIN CUP

This tip has been a game changer! For bakery style muffin tops, line a 12 count muffin pan with 6 muffins liners, meaning you’ll only fill every other muffin well with batter. Filling every other cup allows the muffins to spread and dome without running into each other. This technique also encourages the muffins to brown, creating a golden muffin top.

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

Carrot Muffin Recipe 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!
  • Skip the cream cheese filling and spread cream cheese frosting on the tops!

FAQs for this Recipe for Carrot Cake Muffins

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

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Carrot Cake Muffins Recipe

By: Beth
Prep Time: 15 minutes
Cook Time: 30 minutes
Resting Time: 15 minutes
Total Time: 1 hour
Servings: 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 

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. Place the bowl with the cream cheese filling in the freezer while you prep the rest of the recipe. Chilling the filling will help keep it from melting into the muffins.

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.

Assemble

  • After the 15 minute rest, fill the liners with only 1-2 tablespoons of batter, then add 1-2 tablespoons of the cold cream cheese mixture, then top each muffin with more batter, all the way to the top. The muffin cups should be very full! Be sure to only put 1-2 tablespoons of batter in initially, then add the cream cheese filling. If you add the filling too close to the top of the muffin, it will ooze out the top. Sprinkle the muffins with sanding sugar.
  • Bake for 7 minutes at 425ºF, then keep the muffins in the oven, and turn the temperature down to 350ºF and bake for 12-15 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. Some muffins may have more of a hallow center, where the cream cheese melts into the muffin. But freezing the cream cheese filling before adding it to the batter can help prevent that.
    Repeat with the remaining batter, making sure to bump the temperature back up to 425ºF.

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.

4 Tips for Bakery Style Muffins

Please reference the post for an explanation of why I use each tip. 

1. THE REST PERIOD

Let the batter rest for 15 minutes after it’s mixed and before you scoop it into the muffin pan. 

2. BAKE AT HIGH TEMPERATURE INITIALLY

Bake the muffins at a high temperature (425ºF) initially then lower to 350ºF. 

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.

4. FILL EVERY OTHER MUFFIN CUP

Filling every other cup allows the muffins to spread and dome without running into each other. This technique also encourages the muffins to brown, creating a golden muffin top.

Nutrition

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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About Beth

I believe that everyone should have a go-to dessert to bring to parties! With hundreds of recipes, I'll help you find yours!

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21 Comments

  1. Can I add other add-ins like raisins, pecans or pineapple instead of the cream cheese filling? And would you then take down the amount of carrots? Any thoughts or help is greatly appreciated. Thank you very much looking forward to making these for Easter.

    1. Hi Kelly! You can skip the cream cheese filling without making any adjustments. You can definitely add in raisins or pecans. I would suggest 1-1.5 cups. I don’t recommend adding pineapple, unless it’s dried, because fresh pineapple can add too much moisture.

  2. Soft, dense and perfect texture. Great spice level. I omitted the cream cheese layer and added chopped pecans and raisons. So good!

    I also use almond milk with a ew splashes of lemon juice for an alternative to buttermilk. Works well.