Healthier Cream Cheese Filled Carrot Cake Muffins

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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!

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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.

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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!

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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.

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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!

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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!

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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.

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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.

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Other Muffin Recipes

• Glazed Lemon Poppy Seed Muffins
• Skinny Chocolate Banana Muffins
• Pumpkin Muffins
• Almond Poppy Seed Muffins
• Banana Nut Muffins (Healthier Recipe)
• Mini Blueberry Muffins

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