If you have ever dreamed of biting into a cloud of creamy, airy sweetness, then you are going to love making the Fluffy Japanese Cotton Cheesecake Cupcakes Recipe. These little delights are a perfect blend of cheesecake richness and soufflé-like lightness that melt in your mouth with every bite. Whether you’re looking to impress guests or simply indulge yourself with a comforting treat, this recipe brings together simple pantry ingredients in a way that creates something extraordinary. Let me share this personal favorite that consistently brings smiles and requests for seconds!

Ingredients You’ll Need
Gathering simple but essential ingredients is what makes the Fluffy Japanese Cotton Cheesecake Cupcakes Recipe so approachable and rewarding. Each ingredient plays a crucial role in creating the soft, velvety texture and subtle sweetness that make these cupcakes stand out.
- 5 oz cream cheese, softened: This forms the creamy base and gives the cupcakes their classic cheesecake flavor.
- 1/4 cup whole milk: Adds moisture and helps create a smooth batter.
- 1/4 cup unsalted butter: Provides richness and a tender crumb.
- 3 large eggs, separated: Egg yolks enrich the batter while the egg whites, whipped to stiff peaks, lighten the texture.
- 1/4 cup all-purpose flour: Gives structure without weighing down the cupcakes.
- 1 tbsp cornstarch: Helps stabilize the cake and contributes to the delicate crumb.
- 1/4 cup granulated sugar: Sweetens perfectly and assists in whipping the egg whites.
- 1/4 tsp cream of tartar (optional): Stabilizes the egg whites to maintain fluffiness.
- Powdered sugar, for dusting (optional): Adds a charming finishing touch.
How to Make Fluffy Japanese Cotton Cheesecake Cupcakes Recipe
Step 1: Prepare Your Baking Setup
Start by preheating your oven to 300°F (150°C) and lining a muffin tin with cupcake liners. Place this tin inside a larger baking dish that will be used for a water bath — this technique gently cooks the cupcakes, keeping them moist and soft.
Step 2: Melt the Cream Cheese Mixture
In a heatproof bowl set over simmering water, melt the cream cheese, whole milk, and unsalted butter. Stir until everything is silky smooth, then set aside to cool slightly. This step ensures a lump-free batter, which is crucial for that classic cotton cake texture.
Step 3: Combine Dry Ingredients
Sift together the all-purpose flour and cornstarch to eliminate any clumps. Gently fold these dry ingredients into the cooled cream cheese mixture, taking care not to overmix so the batter stays light and airy.
Step 4: Add the Egg Yolks
Whisk in the egg yolks one at a time until your batter becomes smooth and glossy. This adds richness and helps bind the mixture together beautifully.
Step 5: Whip the Egg Whites
In a clean, grease-free bowl, beat the egg whites until they start to look frothy. Add the cream of tartar, if using, then gradually beat in the granulated sugar until stiff peaks form. Achieving the right consistency here is key — the fluffiness of your cupcakes depends on these clouds of air trapped in the egg whites.
Step 6: Fold in the Egg Whites
Gently fold the whipped egg whites into the cream cheese batter in three additions. Use a spatula to carefully incorporate the whites without deflating them, which preserves that signature soft lift.
Step 7: Prepare for Baking
Divide the light and airy batter evenly among the cupcake liners. Then, pour hot water into the larger baking dish until it comes halfway up the sides of the muffin tin for the water bath. This moist heat is what gives the cupcakes their tender crumb and prevents cracking.
Step 8: Bake the Cupcakes
Bake for 25 to 30 minutes, or until the tops are set and just starting to turn a delicate golden color. Keep an eye on them — you want that perfect balance of lightly browned tops with soft centers.
Step 9: Let Them Rest
Once out of the oven, turn it off and leave the cupcakes inside for 10 minutes with the door slightly ajar. This gradual cooling helps avoid sudden temperature changes that could cause the cupcakes to sink.
Step 10: Chill and Finish
Remove the cupcakes from the water bath and let them cool completely at room temperature before chilling in the fridge for at least an hour. Just before serving, dust with some powdered sugar for a delicate, elegant touch.
How to Serve Fluffy Japanese Cotton Cheesecake Cupcakes Recipe

Garnishes
While these cupcakes are perfect on their own, a light sprinkle of powdered sugar elevates their look beautifully. A few fresh berries or a dollop of whipped cream can add a fresh contrast that pairs wonderfully with their creamy texture.
Side Dishes
Serve your cotton cheesecake cupcakes alongside a cup of green tea or a gentle floral tea like jasmine or chamomile. The subtle flavors of the beverage complement the delicate sweetness of the cake without overpowering it.
Creative Ways to Present
For a whimsical twist, top each cupcake with edible flowers or arrange them on a tiered dessert stand for a fancy gathering. You could also drizzle a bit of matcha glaze or berry coulis to give an extra pop of flavor and color that dazzles the eye and palate.
Make Ahead and Storage
Storing Leftovers
You can store any leftover Fluffy Japanese Cotton Cheesecake Cupcakes Recipe in an airtight container in the refrigerator. They’ll keep beautifully fresh for up to 3 days, maintaining that tender texture and delicate flavor.
Freezing
If you want to enjoy them later, wrap each cupcake individually in plastic wrap and place them in a freezer-safe container or bag. Frozen, they hold up well for up to a month. Just be sure to thaw them gently in the fridge overnight before serving.
Reheating
When ready to eat, reheat the cupcakes at room temperature or warm slightly in a low oven for just a few minutes. Avoid microwaving as it can toughen the soft, airy crumb you worked so hard to achieve.
FAQs
Can I use low-fat cream cheese instead of regular?
While you can try low-fat cream cheese, it may affect the texture and richness of the cupcakes. For the signature fluffiness and smoothness, regular cream cheese is recommended.
Why do these cupcakes need a water bath?
The water bath provides gentle, even heat that prevents the cupcakes from drying out or cracking. It helps maintain their soft, custard-like texture.
Is it necessary to use cream of tartar?
Cream of tartar helps stabilize the egg whites and ensure they hold their shape when folded into the batter. If you don’t have it, you can skip it, but the cupcakes might not be quite as fluffy.
Can I make this recipe dairy-free?
Replacing cream cheese, butter, and milk with dairy-free alternatives is possible, but the texture might differ. Using a soft vegan cream cheese and plant-based milk could work with some experimentation.
How do I know when the cupcakes are done?
They should have a lightly golden top and feel set to the touch but still soft in the center. A toothpick inserted should come out mostly clean with just a few moist crumbs.
Final Thoughts
If you’re ready for a baking adventure that feels both simple and extraordinarily satisfying, I can’t recommend the Fluffy Japanese Cotton Cheesecake Cupcakes Recipe enough. It’s a dreamy dessert that will quickly become a staple in your recipe box, perfect for sharing or savoring solo. Give it a try, and enjoy the gentle, cloud-like magic with every bite!
Print
Fluffy Japanese Cotton Cheesecake Cupcakes Recipe
- Prep Time: 20 minutes
- Cook Time: 30 minutes
- Total Time: 1 hour 60 minutes (including chilling)
- Yield: 8 cupcakes
- Category: Dessert
- Method: Baking
- Cuisine: Japanese
- Diet: Vegetarian
Description
These Fluffy Japanese Cotton Cheesecake Cupcakes are light, airy, and irresistibly soft. Featuring a delicate balance of cream cheese, egg whites, and a gentle water bath baking method, these cupcakes offer a melt-in-your-mouth texture and subtle sweetness. Perfect for an elegant treat or a special dessert, they combine the charm of traditional Japanese cotton cheesecake in a convenient, individual cupcake form.
Ingredients
Cheesecake Base
- 5 oz cream cheese, softened
- 1/4 cup whole milk
- 1/4 cup unsalted butter
- 3 large eggs, separated
- 1/4 cup all-purpose flour
- 1 tbsp cornstarch
- 1/4 cup granulated sugar
- 1/4 tsp cream of tartar (optional)
Topping
- Powdered sugar, for dusting (optional)
Instructions
- Preheat and prepare baking setup: Preheat your oven to 300°F (150°C). Line a muffin tin with cupcake liners and place this tin inside a larger baking dish that will accommodate a water bath.
- Melt cheese mixture: In a heatproof bowl set over simmering water, melt the cream cheese, whole milk, and unsalted butter together, stirring continuously until smooth. Once melted, remove from heat and allow it to cool slightly.
- Combine dry ingredients: Sift the all-purpose flour and cornstarch together to ensure even distribution and then fold these into the cooled cream cheese mixture gently until just combined.
- Add egg yolks: Whisk the egg yolks into the batter mixture until smooth and glossy, creating the base consistency for your cupcakes.
- Beat egg whites: In a clean, dry bowl, begin beating the egg whites until frothy. Add the cream of tartar to stabilize and continue beating gradually incorporating the granulated sugar until you achieve stiff, glossy peaks.
- Fold egg whites into batter: Carefully fold the whipped egg whites into the cream cheese batter in three additions. This gentle folding keeps the mixture airy, essential for the fluffy texture.
- Fill cupcake liners: Spoon or pour the batter evenly into the lined muffin tin.
- Prepare water bath: Pour hot water into the larger baking dish around the muffin tin to about halfway up the sides. This water bath ensures gentle, even baking, preventing cracking and dryness.
- Bake: Bake in the preheated oven for 25-30 minutes, or until the tops are set and lightly golden.
- Rest in oven: Turn off the oven and leave the cupcakes inside for 10 minutes with the door slightly ajar to avoid sudden temperature changes that could cause sinking.
- Cool and chill: Remove the cupcakes and allow them to cool completely at room temperature. Chill them in the refrigerator for at least 1 hour to enhance the texture and flavor.
- Serve: Before serving, dust the tops with powdered sugar if desired for a pretty finish.
Notes
- Using a water bath is crucial for the soft, jiggly texture representative of Japanese cotton cheesecake.
- If cream of tartar is unavailable, a few drops of lemon juice or white vinegar can be used as a substitute to stabilize egg whites.
- Ensure that the egg whites are whipped to stiff peaks for maximum volume in the cupcakes.
- Cool and chill time improves the texture and makes the cupcakes easier to handle and slice if desired.
- These cupcakes are best enjoyed within 2 days if refrigerated and stored in an airtight container.

