Carrot Cake Muffins Recipe With Cheesecake Fillings

Carrot cake muffins with cheesecake fillings are the perfect combination of warm spices, tender cake, and a creamy center. Each muffin is topped with a cinnamon-sugar streusel and a sweet drizzle of glaze, making them irresistible for breakfast, brunch, or dessert. This recipe gives you everything you need to create bakery-style muffins that are moist, flavorful, and delightfully indulgent.

ingredients

for carrot cake muffins

• 2 1/4 cups all-purpose flour
• 1/2 cup granulated sugar
• 1/4 cup light brown sugar (firmly packed)
• 1 1/2 teaspoons baking powder
• 1/4 teaspoon baking soda
• 1 1/2 teaspoons ground cinnamon
• 3/4 teaspoon ground ginger
• 3/4 teaspoon salt
• 2 large eggs
• 3/4 cup water
• 1/3 cup vegetable oil
• 1 cup grated carrots (about 2–3 medium carrots)

for cream cheese filling

• 10 oz cream cheese, softened
• 1/4 cup + 1 tablespoon sugar
• 1/2 teaspoon vanilla

for streusel topping

• 1 cup all-purpose flour
• 2/3 cup granulated sugar
• 1/2 cup unsalted butter, melted
• 1 teaspoon cinnamon
• 1/4 teaspoon salt

for the glaze

• 1 teaspoon milk
• 1/4 cup powdered sugar

instructions

1. Preheat the oven to 400°F and line a standard cupcake pan with paper liners.
2. Make the streusel topping: In a bowl, combine 1 cup flour, 2/3 cup sugar, 1 teaspoon cinnamon, and 1/4 teaspoon salt. Add 1/2 cup melted butter and mix with a fork until crumbly. Set aside.
3. Prepare the cream cheese filling: Beat together cream cheese, 1/4 cup + 1 tablespoon sugar, and 1/2 teaspoon vanilla until smooth. Set aside.
4. Mix dry muffin ingredients: In a large bowl, whisk together flour, sugars, baking powder, baking soda, cinnamon, ginger, and salt.
5. Mix wet muffin ingredients: In a smaller bowl, whisk together eggs, water, and vegetable oil.
6. Combine the wet and dry ingredients until just mixed, then fold in grated carrots.
7. Spoon about 1 1/2 to 2 tablespoons of muffin batter into each cupcake liner to cover the bottom.
8. Add 1 heaping tablespoon of cream cheese filling to the center of each muffin.
9. Top with additional muffin batter until cups are 3/4 full.
10. Sprinkle each muffin with the prepared streusel topping.
11. Bake for 20 minutes or until a toothpick inserted into the muffin part (not the filling) comes out clean.
12. Let muffins cool in the pan for 10 minutes, then transfer to a wire rack to cool completely.
13. Make the glaze: Stir together 1 teaspoon milk and 1/4 cup powdered sugar until smooth.
14. Drizzle glaze over cooled muffins before serving.

serving and storage tips

serving tips

• Serve these carrot cake muffins at room temperature or slightly warm to enjoy the full flavor and soft texture.
• For a bakery-style presentation, drizzle the glaze just before serving.
• Pair with coffee, tea, or a glass of cold milk for a comforting snack or breakfast treat.
• Add a dusting of powdered sugar on top for a festive touch when serving at brunch or special gatherings.
• These muffins make a great addition to Easter brunch, holiday dessert tables, or weekend breakfasts.

storage tips

• Refrigerator: Store muffins in an airtight container in the refrigerator for up to 4 days. Because of the cream cheese filling, refrigeration is necessary.
• Freezer: Wrap each muffin individually in plastic wrap and place them in a freezer-safe container or zip-top bag. Freeze for up to 2 months.
• Thawing: To thaw, place a muffin on the counter for about 1 hour, or microwave it for 20–30 seconds until warmed through.
• Reheating: Warm muffins in the microwave for a few seconds or in a 300°F oven for 5–7 minutes to bring back their soft texture.
• Glaze storage: If you’re storing unglazed muffins, you can keep the glaze in an airtight container in the fridge for up to a week and drizzle it fresh when serving.

variations

1. nut lovers’ carrot muffins
Add 1/2 cup chopped walnuts or pecans to the batter for a nutty crunch that complements the spiced carrot base. You can also sprinkle a few on top of the streusel for extra texture.

2. coconut carrot cheesecake muffins
Fold 1/4 cup sweetened shredded coconut into the muffin batter. The coconut adds tropical flavor and a chewy texture that pairs beautifully with the carrot and cream cheese filling.

3. pineapple-carrot fusion
Mix in 1/4 cup well-drained crushed pineapple to the batter. It adds moisture and a natural sweetness, creating a lighter, tropical twist on the classic.

4. whole wheat version
Swap out half of the all-purpose flour for whole wheat flour. This adds a nutty flavor and increases the fiber content without compromising too much on texture.

5. spiced up muffins
Enhance the warm flavor profile by adding 1/8 teaspoon ground nutmeg and a pinch of ground cloves or allspice. These spices deepen the carrot cake flavor for a more complex, autumnal muffin.

6. zesty orange twist
Stir 1 teaspoon of freshly grated orange zest into the muffin batter. The citrus brightens up the overall flavor and adds a refreshing contrast to the richness of the cheesecake filling.

7. maple-glazed muffins
Instead of the traditional milk glaze, use 1 teaspoon of maple syrup and 1 teaspoon of milk mixed with powdered sugar. This adds a warm, earthy sweetness that pairs beautifully with the spiced muffin.

8. mini muffin bites
Use a mini muffin tin for bite-sized treats. Fill each cavity about halfway, add a small dollop of cream cheese filling, top with batter and streusel, and bake for 12–14 minutes. These are perfect for brunch buffets or kids’ snacks.

9. raisin delight version
Fold 1/4 cup golden or regular raisins into the batter. Soak them in warm water for 10 minutes beforehand to plump them up and ensure they stay moist while baking.

10. gluten-free adaptation
Use a 1:1 gluten-free flour blend in place of all-purpose flour. Be sure to check that your baking powder and other ingredients are certified gluten-free. This version still turns out soft and flavorful with the right flour mix.

FAQs

1. can i make these muffins ahead of time?
Yes, you can prepare them a day in advance. Store them in an airtight container in the refrigerator and glaze them right before serving for the best texture.

2. can i use pre-shredded carrots from the store?
While pre-shredded carrots are convenient, freshly grated carrots provide better moisture and texture for these muffins.

3. what’s the best way to store leftover muffins?
Store in an airtight container in the refrigerator for up to 4 days due to the cream cheese filling. Reheat before serving if desired.

4. can i freeze these muffins?
Yes. Wrap each muffin individually in plastic wrap and place in a freezer bag. Freeze for up to 2 months. Thaw at room temperature or warm in the microwave.

5. do i have to use the streusel topping?
No, the muffins will still be delicious without it, but the streusel adds a sweet, buttery crunch that enhances the flavor and presentation.

6. can i make them without the cream cheese filling?
Yes, you can skip the filling for a simpler carrot muffin, but the cheesecake center adds a rich, creamy contrast that’s worth including.

7. how do i know when the muffins are done?
Insert a toothpick into the muffin portion (not the cream cheese center). If it comes out clean or with a few moist crumbs, they’re done.

8. can i substitute the oil with applesauce?
Yes, you can replace up to half of the oil with unsweetened applesauce for a lower-fat version. The texture may be slightly different, but still moist.

9. are these muffins overly sweet?
No, they’re well-balanced. The carrot batter is mildly sweet, and the cream cheese and glaze add richness without overwhelming the palate.

10. can i turn this recipe into a loaf or cake?
Yes, you can bake it in a greased 9×5 loaf pan or small cake pan. Adjust the baking time to 40–50 minutes and check with a toothpick for doneness.

These carrot cake muffins with cheesecake fillings are a moist, flavorful, and satisfying treat you’ll want to make again and again. With a creamy center, crumbly streusel topping, and sweet glaze, they bring bakery-level indulgence right to your kitchen. Perfect for any occasion, they’re easy to make and even easier to enjoy.

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