Carrot Cake Muffins with Cream Cheese Filling

I’ve been wanting to make carrot cake muffins with cream cheese filling, but I wanted them to feel a little more special. So I took my moist, perfectly spiced carrot cake batter, added a creamy cheesecake filling in the center, and finished them with a buttery crumble on top.

If you’ve made my Carrot Cake Cheesecake or even my Cream Cheese Frosting, this follows that same logic — balance the moisture, control the mixing, and don’t overbake. I tested these specifically as jumbo muffins because I wanted that bakery-style look with a thick center of cheesecake. They also work beautifully as regular muffins (you’ll get 12–14), but I personally love the jumbo size for the proportions alone.

You’re going to love these because…

• The cream cheese center stays creamy, not dry
• The muffin is oil-based, so it stays moist for days
• The crumble gives texture without overpowering
• The spice balance is warm but not heavy
• They work as jumbo or regular muffins

Key Ingredients & Why I Use Them

Oil instead of butter: I use neutral vegetable oil here because I want guaranteed moisture. Carrot muffins can dry out easily. Oil keeps the crumb soft even after refrigeration.

Sour cream (or Greek yogurt): This is non-negotiable for me. It adds richness and keeps the texture tender. I’ve tested with both — they work equally well.

Finely grated carrots: I always grate them fine and lightly pack them. Thick shreds don’t melt into the batter the same way and can create uneven texture.

Block cream cheese: I only use full-fat block cream cheese for the filling. The spreadable kind is too soft and won’t bake properly.

Brown sugar + granulated sugar: Brown sugar adds moisture and depth. A small amount of granulated sugar keeps the crumb from feeling too dense.

Spice blend: Cinnamon is the backbone, but the nutmeg and ginger make it taste like carrot cake — not just “spiced muffins.”

How to Make These Muffins

The full recipe is below in the recipe card, but here’s exactly how I make them step by step.

Step 1: Prep the pan and make the crumble

Preheat to 375°F (190°C). If using convection, bake at 350°F. Line your muffin pan with paper liners — this makes 6 jumbo muffins or 12–14 regular muffins.

Next, let’s make the crumble. I combine the brown sugar, granulated sugar, flour, cinnamon, salt and stir in a small bowl. Then I rub in the softened butter with my fingers until sandy clumps form. I like to refrigerate the crumble while I prepare the batter. Cold crumble gives better texture on top.

Step 2: Make the cream cheese filling

Next, beat the cream cheese for about 1 minute until completely smooth in a medium bowl. This step matters because any lumps that form now will remain.

Step 3: Add the sugar and sour cream

Then I add the sugar and sour cream and mix until creamy.

Step 4: Add the egg and vanila

Add the egg and vanilla and mix just until combined. Stop once it’s smooth. Overmixing incorporates too much air, and that can cause cracking. Set aside.

Step 5: Make the muffin batter

In a large bowl, I whisk together the flour, baking powder, baking soda, spices, and salt.

Step 6: Combine the wet ingredients

In a separate bowl or measuring cup, I whisk the oil, sugars, eggs, sour cream, and vanilla until smooth.

Step 7: Combine the wet ingredients with the dry

Then I add the wet ingredients to the dry ingredients and fold gently. I stop mixing as soon as I don’t see dry streaks. Overmixing with the flour mixture will make the muffins dense. Fold in the finely grated carrots last.

Step 8: Final mixing

If you are adding any additional nuts like I typically do, add them now. I’m adding nuts (½ cup chopped walnuts or pecans). Fold gently!

Step 9: Assemble & bake

Fill each liner about halfway with carrot batter. Add a dollop of cheesecake filling right in the center. Top with more carrot batter until the liners are about ⅔ full. Sprinkle generously with crumble topping.

Bake in the preheated oven based on the size of your muffins. For regular muffins, it can take 18–22 minutes. For jumbo muffins it can take anywhere from 25–30 minutes.

I look for the cake portion to be set and a toothpick inserted into the carrot section (not the cheesecake center) to come out clean. Let them cool completely before glazing on a wire rack. The cheesecake center needs time to fully set.

Step 10: Glaze and serve

When your delicious carrot cake muffins with cream cheese filling have completely cooled, prepare the glaze. To make the glaze, beat the cream cheese, butter, powdered sugar, and 1 tbsp of milk using a hand mixer. You can also use a whisk as long as you can vigorously whisk the mixture.

Once the glaze is smooth, it’s ready. If you notice the glaze is too thick, add the remaining milk, so you are able to drizzle. Pour the glaze over each cooled down muffin. Enjoy!

Variations

Sometimes I like to add…

• Add ½ cup chopped pecans or walnuts
• Swap sour cream for Greek yogurt
• Skip the glaze and dust lightly with powdered sugar
• Add a tiny bit of orange zest to the batter for brightness

If you like carrot desserts in general, you might also enjoy my classic Carrot Cake, Carrot Cupcakes, or even my Red Velvet Cake if you’re in the mood for another classic with cream cheese elements.

Storage & Make Ahead

I store any leftover muffins in the refrigerator in an airtight container because of the cheesecake filling. They keep well for 4–5 days, and I find the texture is actually even better on day two.

If serving, I let them sit at room temperature for about 20–30 minutes so the center softens slightly. You can freeze them (without glaze) for up to 2 months in the freezer. Thaw overnight in the fridge, then glaze before serving.

FAQ

Let me know!

If you make these carrot cake muffins with cream cheese filling, let me know how they turn out. Leave a comment below, leave a star rating, or tag me on Instagram so I can see them — I always love seeing your versions.

Carrot Cake Muffins with Cream Cheese Fillings

Camila Hurst

Moist carrot cake muffins filled with a creamy baked cheesecake center, topped with a buttery crumble and finished with a light cream cheese glaze. These can be made as jumbo bakery-style muffins or standard size, and they stay soft for days thanks to the oil-based batter.

5 from 1 vote

Print Recipe Pin Recipe

Prep Time 25 minutes mins

Cook Time 30 minutes mins

Cooling 1 hour hr

Total Time 1 hour hr 55 minutes mins

Servings 6 jumbo muffins

Calories 580 kcal

Ingredients

 

Crumble Topping

• ¼ cup light brown sugar 60g
• 2 tbsp granulated sugar
• ½ cup + 2 tbsp all-purpose flour 75g
• ⅕ tsp ground cinnamon
• pinch of salt
• ¼ cup unsalted butter 56g

Cheesecake Filling

• 8 oz full-fat cream cheese softened (226g)
• ¼ cup granulated sugar 50g
• ⅓ cup sour cream 80g
• 1 egg
• 1 tsp vanilla extract
• piinch of salt

Carrot Cake Muffin Batter

• 2½ cups all-purpose flour 300g
• 1 ½ tsp baking powder
• ¾ tsp baking soda
• 1½ tsp cinnamon
• ⅜ tsp nutmeg
• ⅜ tsp ginger
• ¾ tsp fine salt
• ¾ cup neutral oil (or melted coconut oil) 180 ml
• ¾ cup brown sugar 150g
• ⅜ cup granulated sugar (6 tbsp) 75g
• 3 large eggs room temperature
• ¾ cup sour cream or Greek yogurt 180g
• 1½ tsp vanilla extract
• 1½ cups fnely grated carrots (lightly packed) 150g

Cream Cheese Glaze

• 3 tbsp cream cheese at room temperature (42g)
• ½ tbsp unsalted butter 7g
• 3-4 tbsp powdered sugar 31
• 1-3 tbsp milk

Instructions

 

• This recipe yields 6 jumbo muffins, or 12-14 regular size ones. Line the pan of your choice with muffin liners and set aside. Preheat the oven to 375°F (190°C).

Crumble Topping

• Combine the brown sugar, granulated sugar, flour, and cinnamon for the topping in a small bowl. Add the softened butter and rub it into the dry ingredients with your fingers or a fork until the mixture forms small, sandy clumps. Set it aside. I like to keep it in the fridge while I make the muffin batter.

Cheesecake Batter

• In a medium mixing bowl, beat the cream cheese for 1 minute until smooth. Add the sugar and sour cream and beat until creamy.
• Mix in the egg yolk and vanilla extract until just combined. Set aside.

Muffin Batter

• In a large bowl, whisk the flour, baking powder, baking soda, spices, and salt. Set aside.
• In a separate bowl, whisk the oil, sugars, eggs, sour cream, and vanilla until smooth.
• Add the wet ingredients to the bowl with the dry ingredients, followed by the carrots.
• Fold to combine. If using nuts, add now.

Assemble & Bake

• Spoon a portion of carrot cake batter into each lined cavity, filling about halfway. Place a dollop of cheesecake batter in the center of each cupcake, then top with another spoonful of carrot cake batter until the liners are about ⅔ full.
• Bake the muffins for 18–22 minutes, or until a toothpick inserted into the cake portion comes out clean. Jumbo muffins will take about 25-30 minutes.
• Remove from the oven and allow the cupcakes to cool completely before adding the glaze.

Cream Cheese Glaze

• To make the glaze, beat the cream cheese, butter, powdered sugar, and 1 tbsp of milk using a hand mixer. You can also use a whisk as long as you can vigorously whisk the mixture.
• Once the glaze is smooth, it’s ready. If you notice the glaze is too thick, add the remaining milk, so you are able to drizzle.
• Pour the glaze over each cooled down muffin.

Notes

Nuts: If desired, you can add ½ cup (50 g) chopped walnuts or pecans to the carrot cake batter.

Cream cheese: Use block cream cheese, not the spreadable kind.

Sour cream: Can be replaced with Greek yogurt.

Baking: If your oven is convection, bake at 350°F.

Pan: I use a pan called Monfish on Amazon. Search for monfish jumbo pan with straight sides and you’ll find it. I use Caperci liners.

Nutrition

Serving: 1muffindCalories: 580kcal

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