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Healthier Cream Cheese Filled Carrot Cake Muffins

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4.05 from 21 votes

Cream Cheese Filled Carrot Cake Muffins are packed with the same flavors as a traditional carrot cake except these are on the healthier side! Stuffed with a creamy cream cheese center and makes a delicious breakfast treat!

PIN these Carrot Cake Muffins to try later!

Cream Cheese Filled Carrot Cake Muffins stacked on top of each-other.Pin

Cream Cheese Filled Carrot Cake Muffins

Carrot Cake Muffins are moist, soft, and made with simple ingredients. These particular muffins are extra special from the rest because the middle of the muffins have a sweet cream cheese filling that takes these muffins to another level.

You can feel good about making these muffins because they are made with healthy ingredients that even kids will love too (my 1 year old sure did!). We use whole wheat flour, coconut oil, coconut sugar, and fresh carrots so they are packed with wholesome ingredients.

Serve these healthy muffins up for breakfast, enjoy them as a snack, or dessert. You can even add a cream cheese frosting to the tops and call them Carrot Cake Cupcakes ;). The warm flavors of vanilla, cinnamon, nutmeg, and ginger shine through and adds just the right amount of spice just as the traditional flavor of carrot cake does.

Other Carrot Cake recipes you’ll love is my Carrot Bundt Cake, Carrot Cake Bars, and Frosted Carrot Cake Cookies.

Carrot cake muffin with cream cheese frosting on top;.Pin

Why You’ll Love This Recipe

  • Healthier muffins: These muffins are made with healthier alternatives so you don’t have to feel guilty about indulging in a few of these.
  • Freezer-friendly: Always have these handy. These muffins freeze well so you can always have some packed away in your freezer.
  • Easy breakfast: Perfect for a grab-and-go breakfast. Make a batch earlier in the week so you always have them ready to go. Both adults and kids will be requesting these!
  • Easy recipe: Bake these muffins for brunches, school lunch boxes, potlucks, picnics, office snacks, Mother’s Day, Easter brunch, or anytime you’re craving muffins. Throw some sprinkles on top if you make these for a party or celebration!
  • Portable: Bring these muffins anywhere by easily placing them in an airtight container or dish wrapped with plastic wrap. They can go and travel anywhere!
Inside of a Cream Cheese Filled Carrot Cake Muffins.Pin

Key Ingredients

  • Cream cheese: Used to make the creamy cream cheese filling. Its best to use full-fat cream cheese and it will easily cream together when it’s softened at room temperature. (You can use low fat or non fat cream cheese but the flavor and texture may be different.
  • Sugar: Adds sweetness. I use a combination of coconut sugar and granulated sugar but you could omit the granulated sugar completely. Just be sure to use an equal amount of coconut sugar. Other healthy alternatives to use instead of granulated sugar is unsweetened applesauce or pure maple syrup.
  • Coconut oil: This is a healthier option but you can also use butter, canola oil, or vegetable oil instead. 
  • Whole large eggs: It’s best if the eggs are at room temperature. They help bind the ingredients together.
  • Vanilla extract: Adds a warm flavor and enhances all the flavors.
  • Flour: Whole wheat flour is used to add a wholesome and nutty flavor. You can also use all-purpose flour or oat flour instead or use a combination of both.
  • Grated carrots: The star ingredient! I highly recommend shredding your own fresh carrots with a box grater to ensure soft and tender muffins. It’s best to use a SMALL HOLE when grating the carrots- the smaller, the better. You’ll need about 3-4 medium carrots.
  • Warm spices: Ground cinnamon, nutmeg, and ginger are used to make the traditional “carrot cake flavor”.
  • Baking powder & baking soda: Used as a leavening to make the muffins rise.
Hoe to make Carrot Cake Muffins process shots.Pin

How To Make Cream Cheese Filled Carrot Cake Muffins

Make cream cheese mixture: In a small mixing bowl with an electric mixer, beat together cream cheese, sugar, and vanilla extract together until smooth. Set aside.

Combine dry ingredients: Preheat oven to 350 degrees F. Line a muffin tin with 12 muffin liners, paper liners, or spray well with nonstick spray. In a medium mixing whisk together the whole wheat flour, baking powder, baking soda, salt, ground cinnamon, nutmeg, and ginger. Set aside.

Combine wet ingredients: In a large mixing bowl mix together the oil, sugars. eggs, and vanilla extract until combined.

Mix muffin batter together: Fold the dry ingredients in with the wet ingredients just until combined with a rubber spatula or wooden spoon, and then fold in the shredded carrots. Do not over-mix.

Add batter and cream cheese to muffin cups: Add 2 tablespoons of carrot cake batter to each muffin liner, then add 1-2 tablespoons of the cream cheese mixture to the center of each muffin. Divide the remaining batter to the top of the muffins. Gently spread the batter with a spoon to cover as much cream cheese mixture as possible.

Bake: Bake muffins for 18-20 minutes or until a toothpick inserted comes out clean. Let cool for a few minutes before transferring to a wire cooling wrack. Enjoy warm or cold!

Cream Cheese Filled Muffins stacked on a plate.Pin

Are Carrot Cake Muffins Healthy?

I’m not a dietician so I can’t technically say..but I can say these muffins make a healthier alternative than your average muffin because they can be made with coconut sugar and coconut oil and they are made with whole wheat flour, and loaded with shredded carrots. SO I would say these are much healthier than any many other muffins out there!

Inside of a carrot cake muffin with cream cheese filling.Pin

Recipe Tips & Variations

  • Don’t squeeze out excess moisture from the carrots. I did this the first time I made these muffins and they came out super dry to say the least. The moisture from the carrots will make these muffins ultra moist and soft with a tender crumb.
  • Protein Muffins: Add a scoop of plain or vanilla flavored protein powder. This will give these muffins an extra protein boost. If you use flavored protein powder it will change the flavor of the muffins.
  • Mini Muffins: If you want these muffins to be bite-sized, add them to a mini muffin pan instead to make Mini Carrot Muffins. Be sure to reduce the baking time to 10-15 minutes since they won’t need as much time to bake.
  • Other Muffin Add Ins: Raisins, chia seeds, flax seeds, cinnamon chips, chocolate chips, chopped nuts, seeds, and sprinkles for fun.
  • Make sure not to over-mix the batter: This will cause the muffins to be dense, rather than light and fluffy. Just stir until all ingredients are combined.
  • Top of the muffins: Add a cream cheese glaze, dust of powdered sugar, frosting, sparkling sugar, or eat them plain as they are! I love smearing the leftover cream cheese filling to the tops with a chopped walnuts and more shredded carrots for color.
Carrot Cake Muffins in a basket.Pin

Leftovers & Storage

Store in refrigerator: Since these muffins have a cream cheese filling, we want to place any leftovers in an airtight container or large zip-lock bag in the refrigerator for up to 5 days. Heat in the microwave before eating to make the muffins soft and warm. You can also just let them come to room temperature for a few minutes. 

Make-Ahead: Muffins are perfect for making ahead because they freeze so well. Once muffins are baked, cool completely, then place the muffin pan in the freezer to flash freeze for at least an hour. Once they are semi-frozen, remove the muffins and place them in a large ziplock bag. Flash freezing them will keep them from sticking together. Make the muffin glaze when ready to eat. 

Freeze & reheating muffins: Place cooled baked muffins in a single layer dish or baking sheet and flash freeze until solid. You can place them in a large zip lock bag (be sure to squeeze our excess air) or an airtight container and freeze for up to two months. When ready to eat, remove from the freezer and let them thaw. Reheat in the microwave or oven for a few minutes.

Frosted carrot cake muffin.Pin

Other Muffin Recipes

Bite mark of Carrot Cake Muffins with cream cheese inside.Pin

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Cream Cheese Filled Carrot Cake Muffins

Cream Cheese Filled Carrot Cake Muffins are packed with the same flavors as a traditional carrot cake except these are on the healthier side! Stuffed with a creamy cream cheese center and makes a delicious breakfast treat!
4.05 from 21 votes
Print Pin Rate
Course: Breakfast, Dessert
Cuisine: American
Keyword: carrot cake muffins, cream cheese filled carrot cake muffins, healthy carrot cake muffins
Prep Time: 15 minutes
Cook Time: 20 minutes
Total Time: 45 minutes
Servings: 12 muffins

Ingredients

Cream Cheese Filling

  • 8 ounce cream cheese softened at room temperature
  • 1/4 cup granulated sugar
  • 1/2 teaspoon vanilla extract

Carrot Cake Muffins

  • 1 1/4 cups whole wheat flour or all purpose flour
  • 1 teaspoon baking powder
  • 1 teaspoon baking soda
  • 1/4 teaspoon salt
  • 1 1/2 teaspoons ground cinnamon
  • 1/4 teaspoon ground nutmeg
  • 1/4 teaspoon ground ginger
  • 1/2 cup vegetable oil or coconut oil
  • 1/3 cup brown sugar or coconut sugar
  • 2 tablespoons granulated sugar
  • 2 whole eggs
  • 1 teaspoon vanilla extract
  • 1 1/2 cups finely grated carrots (don't ring out excess water)

Instructions

  • In a small bowl with an electric mixer, beat together cream cheese, sugar, and vanilla extract together until smooth. Set aside.
  • Preheat oven to 350 degrees F. Line a muffin pan with 12 muffin liners or spray well with nonstick spray. In a medium mixing whisk together the whole wheat flour, baking powder, baking soda, salt, ground cinnamon, nutmeg, and ginger. Set aside.
  • In a large mixing bowl mix together the oil, sugars. eggs, and vanilla extract until combined.
  • Fold the dry ingredients in with the wet ingredients just until combined and then fold in the shredded carrots. Do not over-mix.
  • Add 2 heaping tablespoons of carrot cake batter to each muffin liner, then add 1-2 tablespoons of the cream cheese mixture to the center of the carrot cake batter. Divide the remaining batter to the tops of the cream cheese mixture. Gently spread the batter with a spoon to cover as much cream cheese mixture as possible.
  • Bake muffins for 18-20 minutes or until a toothpick inserted comes out clean. Let cool for a few minutes before transferring to a wire cooling wrack. Frost with leftover cream cheese mixture, walnuts, or leave them plain. Enjoy warm or cold!
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Recipe Rating




10 Comments

  1. 5 stars
    I am a carrot cake lover, so these muffins are right up my alley. Perfect paired with my morning coffee. Great to tuck in the lunchbox too.

  2. 5 stars
    A good carrot cake (muffin) recipe should be a staple in everyone’s kitchen. Your recipe is so moist and full of flavor. The cream cheese adds a decadence to them!

  3. 5 stars
    I love that the cream cheese is in the middle and that there isn’t a ton of sugar. These muffins are a perfect Easter treat for breakfast.

  4. 5 stars
    Wow! These cake muffins look amazingly yummy! It is stuffed with so much cream cheese making it so enticing and tempting! A perfect treat for everyone at any time of the day! Loved it!

  5. 5 stars
    What a great idea! I’m a carrot cake lover and I wanted to try something new. These cupcakes were easy to make, moist and filling them with the cream cheese is genius!

  6. 5 stars
    These muffins seem like a nice treat or snack that everyone will enjoy and I like that they can be frozen and stored for later.

  7. 5 stars
    These muffins are incredibly tasty!! The moistness of the muffins is exquisite, and I particularly enjoy the frosting filling, which adds an element of surprise in every bite.

  8. 5 stars
    These muffins sound like the perfect healthy treat to satisfy my sweet tooth! I can’t wait to try this cream cheese-filled carrot cake muffin recipe. With a healthier twist, it’s guilt-free and still delicious. Yum!