Fluffy Japanese Cotton Cheesecake Cupcakes Recipe
If you’re searching for a dessert that’s both delightfully light and irresistibly dreamy, look no further than Fluffy Japanese Cotton Cheesecake Cupcakes. These pillowy treats are the perfect marriage of cloud-soft sponge and creamy cheesecake, creating an experience that melts on your tongue and keeps you coming back bite after bite. Whether you’re serving them for afternoon tea, a family gathering, or simply indulging in a sweet craving, Fluffy Japanese Cotton Cheesecake Cupcakes bring just the right amount of sweetness and sophistication to your table.

Ingredients You’ll Need
These cupcakes come together with just a handful of everyday ingredients, but each one is essential for their signature airy texture and subtle flavor. Gather these basics and get ready to whip up a batch that will transport you straight to a Japanese café!
- Cream cheese (4 ounces, softened): Go for full-fat for the most luscious, creamy base.
- Whole milk (1/4 cup): Adds moisture and gentle richness, making the texture ultra-soft.
- Unsalted butter (2 tablespoons): Gives a silky mouthfeel and a touch of buttery flavor.
- Egg yolks (3 large): Infuse the batter with color and a luxurious, custardy note.
- Cake flour (1/4 cup, sifted): The finer crumb ensures your cupcakes bake up tender and airy.
- Cornstarch (1 tablespoon): Lightens the crumb and helps achieve that signature cottony texture.
- Salt (1/4 teaspoon): Balances the sweetness and elevates all the flavors.
- Egg whites (3 large): When whipped, they add structure and that iconic soufflé lift.
- Cream of tartar (1/4 teaspoon): Stabilizes the meringue so your cupcakes stay beautifully fluffy.
- Granulated sugar (1/4 cup): Sweetens and helps create glossy, stable peaks in the meringue.
- Powdered sugar (for dusting, optional): Gives a picture-perfect finish with a delicate snowy look.
How to Make Fluffy Japanese Cotton Cheesecake Cupcakes
Step 1: Set Up Your Oven and Water Bath
Start by preheating your oven to 300°F (150°C). Carefully line a standard cupcake pan with paper liners, then nestle the whole pan into a larger baking dish or roasting tray—this will be your magic water bath for perfectly gentle baking!
Step 2: Melt the Cream Cheese Mixture
In a heatproof bowl placed over a pot of simmering water, combine the cream cheese, whole milk, and unsalted butter. Stir gently and patiently until everything melds into a silky, smooth mixture. Remove it from the heat and let it cool slightly before moving on. This step gives you that creamy cheesecake foundation without any lumps.
Step 3: Incorporate Egg Yolks and Dry Ingredients
Whisk the egg yolks into your cooled cream cheese mixture, letting them blend in until the batter is glossy and unified. Sift in the cake flour, cornstarch, and salt, then mix just until no traces of flour remain. This careful blending keeps your base light and lump-free.
Step 4: Whip the Meringue
In a sparkling-clean mixing bowl, beat the egg whites and cream of tartar until foamy. Gradually add the granulated sugar, continuing to beat until the meringue is glossy with soft, billowy peaks. This magical meringue is what gives Japanese Cotton Cheesecake Cupcakes their airy, soufflé-like texture.
Step 5: Fold the Meringue into the Batter
Gently fold the meringue into your cream cheese base in three additions, using a spatula and a light touch. Go slowly and stop folding as soon as the batter is streak-free—this step keeps all the precious fluff intact.
Step 6: Portion and Bake
Divide the finished batter evenly among the cupcake liners. Carefully pour hot water into the larger baking dish so it comes about halfway up the sides of your cupcake pan. Bake for 25 to 30 minutes, then turn off the oven and let the cupcakes sit for 10 more minutes with the oven door slightly ajar, allowing them to cool down gently and avoid collapse.
Step 7: Cool and Garnish
Take the tray out and let your Fluffy Japanese Cotton Cheesecake Cupcakes cool completely before dusting with powdered sugar. These are even better after a rest in the fridge—if you can wait that long!
How to Serve Fluffy Japanese Cotton Cheesecake Cupcakes

Garnishes
Give your cupcakes a classic look with a flutter of powdered sugar, or top them with a swirl of whipped cream, some fresh berries, or even a little lemon zest. The lightness of the cupcakes makes them a wonderful canvas for all sorts of pretty, delicate touches!
Side Dishes
Pair your Fluffy Japanese Cotton Cheesecake Cupcakes with a pot of fragrant green tea or a refreshing iced matcha. For an afternoon tea spread, they shine beside delicate fruit salads or crisp butter cookies. Their subtle sweetness means they won’t overwhelm even the daintiest accompaniments.
Creative Ways to Present
Try arranging your cupcakes on a tiered cake stand for a wow-worthy dessert centerpiece, or gift them in cupcake boxes lined with parchment for an elegant homemade treat. For a festive event, color-code the paper liners and dust each batch with a different garnish—your guests will swoon over both looks and taste!
Make Ahead and Storage
Storing Leftovers
Fluffy Japanese Cotton Cheesecake Cupcakes store wonderfully in the fridge. Place them in an airtight container and they’ll keep their delicate texture for up to three days. Just be sure they’re completely cooled before sealing them away to avoid any sogginess.
Freezing
You can freeze these cupcakes for future snacking! Simply wrap each cooled cupcake individually in plastic wrap, then tuck them into a freezer-safe bag or container. They’ll stay lovely and soft for up to two months—thaw in the fridge overnight when you’re ready to enjoy one again.
Reheating
If you prefer your cheesecake cupcakes a little warmer, you can gently reheat them in the microwave for about 10–15 seconds. This brings back some softness without compromising the fluff. Just don’t overheat or they may lose their signature airy crumb.
FAQs
Why did my Fluffy Japanese Cotton Cheesecake Cupcakes deflate after baking?
This is usually due to either overmixing the batter or removing the cupcakes from the oven too quickly after baking. Be gentle when folding in your meringue, and allow the cupcakes to cool slowly in the oven after baking to keep their lovely height.
Do I really need to use a water bath for this recipe?
Yes, the water bath helps regulate the temperature and provides gentle humidity in the oven, which is crucial for getting that delicate, soufflé-like rise and texture. It’s the secret to baking success with these cupcakes!
Can I add flavors to the basic recipe?
Absolutely! Try adding a few drops of vanilla extract or some fresh lemon zest to the batter for a delicious twist. These subtle additions play beautifully with the light cheesecake base.
Can I use all-purpose flour instead of cake flour?
You can, but cake flour really does make a difference by keeping the crumb ultra-tender and light. If all you have is all-purpose, sift it first and use a tablespoon less for each 1/4 cup to get a similar effect.
How do I know when the cupcakes are done?
The tops should be just set and slightly springy to the touch, without any browning. If you gently jiggle the pan, the cupcakes should look stable, not wobbly. A wooden skewer inserted in the center should come out mostly clean.
Final Thoughts
There’s something truly enchanting about sharing a batch of Fluffy Japanese Cotton Cheesecake Cupcakes with friends and family—each bite is a celebration of softness and subtle flavor. Give this recipe a try and watch as everyone falls for its unique charm. Happy baking!
Print
Fluffy Japanese Cotton Cheesecake Cupcakes Recipe
- Total Time: 50 minutes
- Yield: 8 cupcakes 1x
- Diet: Vegetarian
Description
These Fluffy Japanese Cotton Cheesecake Cupcakes are light, airy, and delicately sweet, making them a delightful treat for any occasion.
Ingredients
Cheesecake Mixture:
- 4 ounces cream cheese, softened
- 1/4 cup whole milk
- 2 tablespoons unsalted butter
- 3 large egg yolks
- 1/4 cup cake flour, sifted
- 1 tablespoon cornstarch
- 1/4 teaspoon salt
Meringue:
- 3 large egg whites
- 1/4 teaspoon cream of tartar
- 1/4 cup granulated sugar
Additional:
- Powdered sugar, for dusting (optional)
Instructions
- Preheat the oven: Preheat the oven to 300°F (150°C). Line a cupcake pan with paper liners and place it in a larger baking dish for a water bath.
- Melt the mixture: In a heatproof bowl over simmering water, melt the cream cheese, milk, and butter until smooth. Remove from heat and cool slightly.
- Prepare the batter: Whisk in egg yolks, then sift in cake flour, cornstarch, and salt. Mix until smooth.
- Whip the meringue: In a clean bowl, beat egg whites and cream of tartar until foamy. Gradually add sugar and beat until soft peaks form.
- Combine and bake: Gently fold the meringue into the cream cheese mixture. Divide batter into cupcake liners. Create a water bath and bake for 25–30 minutes. Let cool in the oven before dusting with powdered sugar.
Notes
- For extra flavor, add a drop of vanilla or lemon zest to the batter.
- Chill the cupcakes for a few hours before serving for the best texture.
- Avoid overmixing to maintain the cupcakes’ light and airy texture.
- Prep Time: 20 minutes
- Cook Time: 30 minutes
- Category: Dessert
- Method: Baking
- Cuisine: Japanese
Nutrition
- Serving Size: 1 cupcake
- Calories: 120
- Sugar: 7g
- Sodium: 90mg
- Fat: 7g
- Saturated Fat: 4g
- Unsaturated Fat: 2g
- Trans Fat: 0g
- Carbohydrates: 10g
- Fiber: 0g
- Protein: 3g
- Cholesterol: 65mg