Carrot Cake Muffins with Cheesecake Filling

Warm, spiced batter and a creamy cheesecake surprise meet in every bite of these Carrot Cake Muffins with Cheesecake Filling. I developed this version after testing it eight times to balance sweetness, moisture, and a stable cheesecake center. The muffins stay tender without a soggy filling because the cream cheese is mixed to a thicker custard and briefly chilled before baking. These are ideal for brunch, lunchboxes, or a small dessert tray — and they travel well to potlucks. If you love variations on carrot cake, try a Brazilian carrot cake for inspiration while you bake. Brazilian carrot cake shows a different texture and flavor profile you might enjoy. Read on for the full recipe, precise measurements, and pro tips that keep the filling centered and the crumb tender.

Why This Recipe Works

The cheesecake filling is thickened with an egg yolk, so it holds shape and won’t sink through the batter.
Brown sugar and oil keep the crumb moist without needing butter, which helps shelf life.
Grated carrots add moisture and sweetness while the short mixing time protects gluten from overdevelopment.
Spices (cinnamon, nutmeg, ginger) are balanced so they enhance, not overwhelm, the cream cheese tang.
Testing across different flours confirmed that all-purpose flour gives the most consistent rise and texture.

Ingredients Breakdown

All-purpose flour — 250 g (2 cups). The structure of the muffins comes from this; do not substitute whole-wheat without adjusting liquids.
Leaveners — 1 1/2 tsp baking powder and 1 tsp baking soda. Baking powder makes lift; baking soda reacts with the acidic yogurt and carrots for browning.
Spices — 1 tsp ground cinnamon, 1/2 tsp ground nutmeg, 1/2 tsp ground ginger. These give classic carrot cake flavor; omit nutmeg for a milder profile.
Salt — 1 tsp fine salt. If you use Morton’s kosher salt, use the full amount; if using Diamond Crystal, reduce to 3/4 tsp.
Sugars — 150 g (3/4 cup) packed light brown sugar + 50 g (1/4 cup) granulated sugar. Brown sugar adds molasses depth; the granulated sugar helps structure.
Oil — 120 ml (1/2 cup) neutral oil (canola or vegetable). Oil keeps the muffins tender and stores better than butter.
Yogurt — 120 ml (1/2 cup) plain Greek yogurt. Adds acidity and moisture; you can substitute sour cream with a slight tang increase.
Eggs — 2 large eggs, room temperature. Eggs build structure and enrich the batter.
Carrots — 250 g (about 2 cups) finely grated carrots. Finely grate for even distribution and moisture.
Add-ins (optional) — 100 g (1/2 cup) chopped walnuts or 60 g (1/4 cup) raisins. Walnuts add crunch; raisins add chew and sweetness.
Cheesecake filling — 227 g (8 oz) cream cheese, softened; 50 g (1/4 cup) granulated sugar; 1 large egg yolk; 1/2 tsp vanilla extract. This makes a dense custard that bakes into a creamy center.
Substitution notes: You can swap Greek yogurt for sour cream, but the tang will be a bit brighter. For a dairy-free version, see Variations & Substitutions below. For a seasonal twist, try pairing techniques from a pumpkin cheesecake recipe for fall flavors: pumpkin cheesecake.

Essential Equipment

12-cup standard muffin tin. A jumbo or mini tin will change baking times.
Muffin liners or nonstick spray. Liners help release and keep muffins neat.
Two medium bowls and one small bowl for the filling. Separate bowls speed assembly.
Box grater or food processor to grate carrots finely and evenly. A food processor saves 3–5 minutes.
Piping bag or resealable plastic bag with corner snipped to fill centers precisely; a spoon works in a pinch.
Instant-read thermometer (optional) to check muffin doneness if desired. You can also use a toothpick.
For a classroom-style trick used in buns and small pastries, the same piping technique in apple cheesecake buns can make filling neater and faster for batches.

Step-by-Step Instructions

Makes 12 muffins | Prep: 25 minutes · Cook: 18–22 minutes · Inactive Time: None · Total: ~47 minutes · Serves: 12 (1 muffin each)

Step 1: Preheat and prep

Preheat the oven to 180°C (350°F). Line a 12-cup muffin tin with liners or grease the cups. Chill the cream cheese if not using right away.

Step 2: Make the cheesecake filling

In a small bowl, beat 227 g (8 oz) softened cream cheese with 50 g (1/4 cup) granulated sugar until smooth, 30–60 seconds. Add 1 large egg yolk and 1/2 tsp vanilla; mix until glossy. Chill 10 minutes to firm, about 10 minutes, so the filling holds its shape when piped.

Step 3: Combine dry ingredients

Whisk 250 g (2 cups) all-purpose flour, 1 1/2 tsp baking powder, 1 tsp baking soda, 1 tsp ground cinnamon, 1/2 tsp ground nutmeg, 1/2 tsp ground ginger, and 1 tsp fine salt in a medium bowl for 15–20 seconds. Set aside.

Step 4: Whisk wet ingredients

In a second bowl, whisk 150 g (3/4 cup) packed light brown sugar, 50 g (1/4 cup) granulated sugar, 120 ml (1/2 cup) neutral oil, 120 ml (1/2 cup) Greek yogurt, 2 large eggs, and 1 tsp vanilla until smooth, about 30–45 seconds.

Step 5: Fold in carrots and add-ins

Stir the wet mixture into the dry ingredients with a spatula until just combined, about 10–12 strokes. Fold in 250 g (2 cups) finely grated carrots and optional 100 g (1/2 cup) chopped walnuts or 60 g (1/4 cup) raisins. Do not overmix — stop as soon as no dry flour is visible.

Step 6: Fill muffin cups

Spoon batter into muffin cups to fill each about two-thirds full, about 30–45 seconds per pan. Pipe or spoon 1 tablespoon of cheesecake filling into the center of each cup, pressing it gently down so it nests within the batter. Top with a small additional spoonful of batter if the filling rises above the batter level.

Step 7: Bake

Bake at 180°C (350°F) for 18–22 minutes, rotating the pan halfway at 10 minutes. Bake until muffin tops are golden and a toothpick into the cake part (not the filling) comes out with a few moist crumbs, about 18–22 minutes; internal temp should read 95°C (203°F) in the cake portion if using a thermometer. Remove from oven and cool in the pan 5 minutes.

Step 8: Cool and serve

Transfer muffins to a wire rack and cool at least 20 minutes before serving so the cheesecake centers set. Serve warm or at room temperature. Active cooling time 20 minutes.

Expert Tips & Pro Techniques

Common mistake: soggy centers happen when the filling is too loose. Chill the filling 10 minutes before piping to firm it and prevent sinking.
Use a piping bag for the filling for consistent centers; a spoon works but may result in uneven pockets.
Make-ahead: Bake, cool completely, then refrigerate in a single layer for up to 48 hours or freeze for longer storage (see Storage & Reheating).
Professional trick: Beat the cream cheese until very smooth then pass it through a fine-mesh sieve for ultimate silkiness in the filling. This is a technique used in professional cheesecakes and adapted here for small batches. For a richer note, try flavoring the filling with 1 tsp grated orange zest or a splash of liqueur from a recipe like a Baileys cheesecake when hosting adults: Baileys cheesecake.
For uniform muffins, weigh batter per cup (about 60–65 g per cup) or use an ice cream scoop for consistent portions.

Storage & Reheating

Refrigerator: Store cooled muffins in an airtight container for 3–4 days. Place a paper towel under the lid to absorb any moisture.
Freezer: Freeze in a single layer on a baking sheet until firm, about 1 hour. Transfer to a freezer bag and freeze up to 3 months. Thaw overnight in the fridge.
Reheating: Reheat from chilled in a 175°C (350°F) oven for 8–10 minutes. From frozen, reheat for 12–15 minutes. Avoid microwaving for long — it can make the crumb gummy and the cheesecake center overly soft.

Variations & Substitutions

Gluten-Free Version: Replace 250 g (2 cups) all-purpose flour with 250 g (2 cups) 1:1 gluten-free flour blend and add 1/2 tsp xanthan gum if the blend lacks it. Baking time increases by 2–4 minutes.
Vegan Version: Use a vegan cream cheese and swap eggs with 2 tbsp ground flaxseed + 6 tbsp water (let sit 10 minutes). Replace yogurt with a dairy-free yogurt and use 120 ml (1/2 cup) applesauce plus 60 ml (1/4 cup) neutral oil to replace eggs and yogurt. Texture will be slightly denser.
Spiced Orange Carrot Muffins: Add 1 tbsp orange zest to the batter and 1/4 tsp ground cardamom; keep the cheesecake filling plain. Baking time unchanged.
Mini Muffins: For 36 mini muffins, reduce baking time to 10–12 minutes and check early for doneness. Use smaller portions of filling (about 1 tsp) per cup.
Cheesecake swirl: Instead of a center, dollop cheesecake filling on top and use a skewer to create a swirl; bake the same time. For inspiration on layered carrot-cheesecake desserts, see this carrot cake cheesecake adaptation: carrot cake cheesecake dessert.

Serving Suggestions & Pairings

Coffee or chai tea — the warm spices pair beautifully with a medium roast coffee or spiced chai.
Citrus cream cheese frosting — pipe a thin smear of frosting and top with toasted walnuts for a dessert-style presentation.
Fresh fruit — serve with sliced pears or orange segments for a bright contrast.
Brunch platter — include savory items like mini quiches and a bowl of yogurt with granola. These muffins pair well with lighter brunch items such as our apple cheesecake buns for a themed spread.

Nutrition Information

Serving size: 1 muffin — Yield: 12 muffins
Estimated per serving: Calories 380 kcal; Total Fat 20 g; Saturated Fat 7 g; Cholesterol 60 mg; Sodium 180 mg; Total Carbohydrates 44 g; Dietary Fiber 2 g; Sugars 22 g; Protein 5 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 dry?
A: Most often you overbaked or overmixed the batter. Bake until a toothpick into the cake portion has a few moist crumbs. Do not overmix — fold until just combined.

Q: Can I make this without eggs?
A: Yes. Use a flax or chia egg (1 tbsp ground flax + 3 tbsp water per egg). Expect a slightly denser crumb and extend baking time by 2–4 minutes.

Q: Can I double this recipe?
A: Yes. Use two muffin tins or bake in batches. If doubling, mix in two bowls to avoid overmixing and rotate pans for even baking.

Q: Can I prepare this the night before?
A: Yes. Make the batter and cheesecake filling, keep both covered in the fridge overnight, then assemble and bake the next day. Bring the batter to room temperature 20–30 minutes before baking.

Q: How long do these keep in the fridge?
A: Store in an airtight container for 3–4 days. The cheesecake filling holds up well chilled.

Q: My cheesecake centers sank. What happened?
A: The filling may have been too loose or too warm when baked. Chill the filling 10 minutes before piping and avoid overfilling the cups.

Q: Can I make mini or jumbo muffins?
A: Yes. Mini muffins bake 10–12 minutes; jumbo muffins take 25–28 minutes. Adjust fill levels to prevent overflow.

Conclusion

If you want extra ideas and variations for similar recipes, these two resources offer alternate cheesecake-filled muffin techniques and flavor ideas: Carrot Cake Muffins Recipe With Cheesecake Fillings and Carrot Cake Muffins with Cream Cheese Filling – Pastry & Beyond. Enjoy baking, and remember the key: a slightly chilled filling and a gentle hand when mixing will give you perfect, creamy-centered muffins every time.