Carrot Cake Muffins with Cheesecake Filling

Warm spice, tender crumb, and a tangy cheesecake center—these muffins hit all the cozy notes. Carrot Cake Muffins with Cheesecake Filling bring the best of carrot cake into a single, portable bite that’s soft enough to sink your teeth into and rich enough for dessert. After testing this version eight times with different grating techniques and flour blends, I settled on a batter that stays moist and a filling that won’t sink or leak. I developed and refined the method while staging pastry shifts at a busy bakery, so the steps are practical for a home kitchen. Read on for precise measures, timing, and pro tips to bake consistently perfect muffins.

Why this recipe works

The batter balances oil and eggs to lock in moisture without making the crumb greasy.
Grating carrots finely disperses moisture and natural sweetness so they bake into the muffin, not sit on the bottom.
A stabilized cheesecake filling (lightened with a bit of sour cream) holds shape and creates a neat center.
Acid (buttermilk) reacts with baking soda for lift while adding a subtle tang that plays well with spices.
Chilling the filling briefly prevents it from bleeding into the batter during baking.

Ingredients breakdown

All-purpose flour — 250 g (2 cups): Provides structure. Do not swap for cake flour without adjusting liquid.
Granulated sugar — 200 g (1 cup): Sweetens and tenderizes. Can reduce by 25 g (2 tbsp) for less sweetness.
Light brown sugar — 50 g (1/4 cup, packed): Adds moisture and a mild caramel note.
Baking powder — 8 g (1¼ tsp) and baking soda — 5 g (1 tsp): Leavening mix gives oven rise and a soft crumb.
Kosher salt — 5 g (1 tsp): Enhances flavor. If using Morton’s kosher, use 3/4 tsp.
Ground cinnamon — 5 g (1 tsp), ground nutmeg — 1 g (1/4 tsp), ground ginger — 1 g (1/4 tsp): Spice trio. Adjust to taste.
Eggs — 2 large (about 100 g total): Bind and leaven.
Vegetable oil — 120 ml (1/2 cup): Keeps crumb tender. Can substitute light olive oil for a subtle fruitiness.
Buttermilk — 240 ml (1 cup): Reacts with baking soda for lift and tender crumb. If unavailable, use 240 ml (1 cup) milk + 1 tbsp lemon juice, let sit 5 minutes.
Vanilla extract — 10 ml (2 tsp): Flavor enhancer.
Carrots — 300 g (3 medium carrots), finely grated: Adds moisture and texture. Peel and grate by hand or on the small holes of a box grater.
Crushed pineapple (optional) — 100 g (1/2 cup), well drained: Adds sweetness and moisture; include only if you want a brighter flavor.

Cheesecake filling

Cream cheese — 225 g (8 oz), full-fat, room temperature: Base of the filling. Do not use low-fat or whipped or filling will be runny.
Granulated sugar — 30 g (2 tbsp): Sweetens the filling.
Sour cream — 30 g (2 tbsp): Lightens and stabilizes texture.
Egg yolk — 1 large: Helps set the center.
Vanilla extract — 2.5 ml (1/2 tsp): Flavor.

Ingredient substitution notes

Greek yogurt may replace sour cream 1:1, but expect a tangier filling.
For gluten-free: use a 1:1 GF blend and add ½ tsp xanthan gum. Baking time may increase by 3–5 minutes.
If you use a different kosher salt brand, weigh it for accuracy.

Essential equipment

12-cup standard muffin tin and 12 paper liners: Paper liners make removal easier; skip liners with nonstick spray.
Electric mixer (hand or stand): Speeds filling smoothing. Whisk and elbow grease work for both batter and filling.
Box grater or food processor with grating disk: For finely grated carrots. A coarse grate makes the muffins more rustic.
Digital scale for dry ingredients: Weighing improves consistency.
2 mixing bowls and a small bowl for filling: Keep wet and dry ingredients separate.
Toothpick or cake tester: Checks doneness through the cake portion (avoid piercing the filling).
Cooling rack: Promotes even cooling.

Step-by-step instructions

Prep Time 20 minutes, Cook Time 20–24 minutes, Inactive Time 15 minutes chilling, Servings 12 muffins.

Step 1: Make the cheesecake filling

In a bowl, beat 225 g (8 oz) cream cheese until smooth, about 1–2 minutes. Add 30 g (2 tbsp) sugar, 30 g (2 tbsp) sour cream, 1 egg yolk, and 2.5 ml (1/2 tsp) vanilla; mix until glossy and smooth, 30–45 seconds. Chill the filling for 15 minutes to firm it slightly; it should hold shape when scooped.

Step 2: Preheat and prepare the pan

Preheat oven to 180°C (350°F) and line a 12-cup muffin tin with liners. Lightly spray liners with nonstick spray if desired to prevent sticking, about 10 seconds per liner. Position a rack in the center of the oven for even heat.

Step 3: Combine dry ingredients

Whisk together 250 g (2 cups) all-purpose flour, 200 g (1 cup) granulated sugar, 50 g (1/4 cup) light brown sugar, 8 g (1¼ tsp) baking powder, 5 g (1 tsp) baking soda, 5 g (1 tsp) kosher salt, 5 g (1 tsp) ground cinnamon, 1 g (1/4 tsp) nutmeg, and 1 g (1/4 tsp) ginger in a large bowl for 30 seconds to evenly distribute.

Step 4: Mix wet ingredients

In another bowl, whisk 2 large eggs for 20–30 seconds, then add 120 ml (1/2 cup) vegetable oil, 240 ml (1 cup) buttermilk, and 10 ml (2 tsp) vanilla; whisk until combined, about 15 seconds. Stir in 300 g (3 medium) finely grated carrots by hand until evenly folded, about 20–30 seconds.

Step 5: Combine wet and dry

Pour wet into dry and fold gently with a flexible spatula for 20–30 strokes. Do not overmix — stop as soon as no dry flour streaks remain. The batter should be thick but spoonable; aim for visible flecks of carrot and a glossy sheen.

Step 6: Fill tins and add filling

Spoon batter into liners, filling each to about 2/3 full, roughly 30–35 g (2 tbsp) batter each. Add 1 heaping teaspoon (about 20 g) of chilled cheesecake filling into the center of each muffin so it sits slightly below the batter surface. Top with an additional 1–2 tablespoons of batter to cover the filling.

Step 7: Bake

Bake at 180°C (350°F) for 20–24 minutes, rotating pan once at 12 minutes for even color. Muffins are done when tops are golden, edges spring back to touch, and a toothpick inserted into the cake portion (avoid the filling) comes out with moist crumbs, about 22 minutes. Allow internal temperature to reach roughly 85°C (185°F) if using an instant-read probe in the cake portion.

Step 8: Cool and serve

Cool muffins in the tin for 8–10 minutes, then transfer to a wire rack to cool to warm, about 30 minutes. Chilling for 30 minutes will make the cheesecake center firmer for transport.

Expert Tips & Pro Techniques

Use room-temperature cream cheese and eggs — they incorporate more smoothly and reduce lumps in the filling.
Common mistake: overfilling liners. Leave headspace for rise or the filling will push out. Fill to 2/3 full and then add filling.
To prevent the filling from sinking to the bottom, chill it until slightly firm and place it into wells of batter rather than onto the bottom of the tin.
Make-ahead: Bake the muffins, cool completely, then freeze on a tray for 2 hours. Transfer to a freezer bag for up to 3 months. Thaw in the fridge overnight or at room temperature for 1–2 hours.
Professional trick: Use a small scoop for batter and a 1-teaspoon scoop for filling to keep portions consistent and baking even.
If you want a swirl effect without a separate filling, dollop filling on top of batter and use a toothpick to swirl; reduce filling by one-third to prevent leaking.

Storage & Reheating

Refrigerator: Store cooled muffins in an airtight container for up to 4 days. Place a sheet of parchment between layers to prevent sticking.
Freezer: Freeze individually on a tray until solid, then move to a labeled freezer bag for up to 3 months. Thaw overnight in the fridge.
Reheating: Reheat from chilled in a 160°C (325°F) oven for 8–10 minutes. For frozen muffins, thaw completely and warm for 6–8 minutes. Avoid microwaving for more than 20–30 seconds as the filling can become rubbery.

Variations & Substitutions

Gluten-free version: Replace 250 g all-purpose flour with a 1:1 GF blend and add ½ tsp xanthan gum. Increase bake time by 3–5 minutes and check doneness with a toothpick.
Lower-sugar option: Reduce granulated sugar to 160 g (3/4 cup) and brown sugar to 25 g (2 tbsp). Expect slightly tighter crumb.
Pineapple-carrot muffins: Fold 100 g (1/2 cup) well-drained crushed pineapple into batter and omit sour cream in the filling. Baking time remains the same.
Vegan adaptation: Use flax eggs (2 tbsp ground flax + 6 tbsp water), replace oil with mild-tasting oil, use vegan cream cheese and yogurt in filling; bake time may increase by 2–4 minutes.
Spice-forward: Double the cinnamon to 2 tsp and add 1/4 tsp cloves for a warmer profile; keep other measurements the same.

Serving suggestions & pairings

Serve warm with a cup of chai tea or drip coffee for a cozy pairing.
Top with a light dusting of powdered sugar and a sprinkle of toasted walnuts for crunch.
Pair with a citrusy yogurt parfait to balance richness and add freshness.
For a dessert board, place these muffins beside strawberry cheesecake bars and fruit for variety.

Nutrition information (per serving)
Serving size: 1 muffin. Yield: 12 muffins.

Calories: 370 kcal
Total Fat: 19 g
Saturated Fat: 9 g
Cholesterol: 80 mg
Sodium: 220 mg
Total Carbohydrates: 43 g
Dietary Fiber: 2.5 g
Sugars: 26 g
Protein: 6 g

Nutrition values are estimates. Actual values may vary based on specific ingredients and preparation methods.

Frequently Asked Questions
Q: Why did my muffins turn out dense instead of fluffy?
A: Likely overmixing the batter or old baking soda/powder. Fold until just combined and check your leaveners; replace if more than 6 months old.

Q: Can I make these without eggs?
A: Yes. Use two flax eggs (2 tbsp ground flax + 6 tbsp water) for binding. Texture will be slightly denser and bake time may increase by 2–3 minutes.

Q: Can I double this recipe?
A: Yes. Use two muffin tins or bake in batches. Do not overfill pans; follow the same portioning. Oven space and air circulation affect baking, so rotate pans if needed.

Q: Can I prepare this the night before?
A: You can make the filling and batter the night before. Store batter tightly covered in the fridge and stir gently before portioning. Bring batter up to cool-room temperature (15–20 minutes) before baking.

Q: How long do these muffins keep in the fridge?
A: Store in an airtight container for up to 4 days. For best texture, eat within 2–3 days.

Q: Why did my cheesecake center leak during baking?
A: Filling that’s too warm or too loose will spread. Chill the filling for 10–15 minutes and use room-temperature cream cheese, but don’t over-whip the filling.

Q: Can I use pre-shredded carrots?
A: You can, but pre-shredded carrots are often drier and may have a coating to prevent clumping. Freshly grate for the best texture and moisture distribution.

Conclusion
These muffins are a great way to serve classic carrot cake in a snackable form while keeping a creamy surprise inside. If you want another take on filled, hand-sized treats, try the Carrot Cake Muffins Recipe With Cheesecake Fillings for inspiration. For a slightly different cream-cheese-filled muffin, see the version at Carrot Cake Muffins with Cream Cheese Filling – Pastry & Beyond.