Japanese Cotton Cheesecake Cupcakes

Japanese cotton cheesecake cupcakes came into my life on a quiet afternoon when I wanted something light and comforting but didn’t want to commit to baking a whole cheesecake and I had a bit of cream cheese in the fridge and a few eggs to spare so I whipped up a small batch just to experiment and the moment I took that first airy bite I was hooked.

They’ve since become one of my favorite treats to make for friends and gatherings because they look so elegant yet feel so soft and melt-in-your-mouth delicate and I love how they’re not overly sweet and dusted with powdered sugar they always make people smile and ask for the recipe.

Ingredients

Here’s what I use for this recipe. You can always make substitutions if you prefer!

• Cream cheese – Creates the creamy and slightly tangy base
• Milk – Loosens the batter and keeps it smooth and silky
• Unsalted butter – Adds richness and helps bind the batter
• Eggs – Separated to create both structure and fluffiness
• Cake flour – Keeps the texture extra light and soft
• Cornstarch – Helps stabilize the structure without adding weight
• Sugar – Lightly sweetens both the yolk base and the meringue
• Lemon juice – Balances the sweetness and helps the egg whites whip beautifully
• Vanilla extract – Adds a delicate warmth to the flavor
• Powdered sugar – A simple finishing touch for presentation

Tools You’ll Need

• Mixing bowls – Separate ones for the yolk mixture and egg whites
• Hand mixer or stand mixer – Essential for whipping the meringue to stiff peaks
• Spatula – For gently folding in the meringue without deflating the batter
• Muffin pan – For shaping and baking the individual cheesecakes
• Cupcake liners – Keeps the cupcakes from sticking and gives them clean edges
• Fine mesh sieve – For dusting powdered sugar on top
• Baking tray and water bath – Helps create a gentle steamy environment for even rise

Instructions

Step 1: Prep the base

I begin by preheating the oven to 300°F (150°C) and lining a muffin tin with paper cupcake liners and I also boil water for the water bath which helps bake the cakes gently.

Step 2: Melt and mix

In a heatproof bowl over a pot of simmering water I melt the cream cheese, butter, and milk while stirring until smooth and then I remove it from heat and let it cool slightly.

Step 3: Add yolk ingredients

Once the mixture is cool I whisk in the egg yolks one at a time followed by vanilla extract then I sift in the cake flour and cornstarch and stir just until combined.

Step 4: Make the meringue

In a clean bowl I beat the egg whites with lemon juice until foamy then slowly add sugar while beating to stiff glossy peaks and this meringue gives the cupcakes their lift.

Step 5: Fold the batter

I take one-third of the meringue and mix it into the yolk batter to loosen it and then gently fold in the rest using a spatula until smooth and airy without overmixing.

Step 6: Fill and bake

I divide the batter evenly among the cupcake liners then place the muffin tin into a larger baking tray filled with about 1 inch of hot water and bake for 25–30 minutes or until set and lightly golden.

Step 7: Cool and dust

After baking I let them cool in the pan for 10 minutes then transfer them to a rack and once fully cooled I dust them lightly with powdered sugar.

Tips

I always strain the yolk batter through a sieve before folding in the meringue for extra smoothness

Don’t open the oven door too early or the cupcakes might deflate

These taste best chilled so I often let them rest in the fridge before serving

You can add a touch of citrus zest for extra brightness

They freeze well too – just wrap individually and thaw before enjoying

Ways to Serve

Serve with fresh berries and whipped cream for a light dessert

Add a dollop of fruit compote or jam for a sweet twist

Enjoy with green tea or coffee for a gentle afternoon treat

Pack into lunch boxes for a special surprise

Serve plain with a dusting of powdered sugar – they don’t need much!

Frequently Asked Questions

What are Japanese Cotton Cheesecake Cupcakes made of?

Japanese cotton cheesecake cupcakes are made with cream cheese, whipped egg whites, cake flour, and a few simple ingredients that create a fluffy, soufflé-like texture.

Why do they need a water bath?

The water bath helps regulate oven temperature and adds moisture so the cupcakes rise evenly and stay soft without cracking or collapsing.

Can I make these ahead of time?

Yes! I often make them a day in advance and store them in the fridge where they stay fresh and fluffy for up to 3 days.

Do I need to use cake flour?

Cake flour gives the lightest result but if you don’t have it you can substitute with all-purpose flour and a bit of cornstarch.

See You in the Kitchen

I hope you try these Japanese cotton cheesecake cupcakes! They’re such a sweet little bite of comfort and always a hit no matter who I serve them to. Let me know how yours turn out and don’t forget to snap a picture before they disappear!

Happy Cooking!

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