Home Desserts Japanese Cotton Cheesecake Cups (GF)

Japanese Cotton Cheesecake Cups (GF)

by momen
Published: Last Updated on
Japanese cotton cheesecake cups gluten free

Japanese cotton cheesecake cups gluten free

If you have tried a whole Japanese cotton cheesecake, you might know how difficult to make it just like a picture of the recipe. It often doesn’t end up how I hope they would, even if I completely followed the recipes. I think this is because slight temperature differences of home ovens easily affect how to bake the whole cheesecake. So you may need to adjust your oven temperature to strive for the beautiful look of the whole cotton cheesecake. Also, there are many preparations needed before put it in the oven.

On the other hand, making cotton cheesecake cups is much easier, quicker, and more simple recipe. But it’s the same taste and texture. They are just smaller in size.

A whole Japanese cotton cheesecake can be a good choice for special occasions. But if you’re planning more casual desserts, you might want to try my Japanese cotton cheesecake cups.

Japanese cotton cheesecake cups gluten free

This recipe makes 12 mini cotton cheesecake with a normal sized muffin pan.

How to make Japanese cotton cheesecake cups

Firstly, I will specify why cotton cheesecake cups are quicker to make than a whole cotton cheesecake. Basic instructions are same, but you can skip the steps below.

Unnecessary steps

  1. Cut parchment paper
  2. Coat the pan and the parchment paper with oil
  3. Dust powdered sugar over the parchment paper
  4. Cover the bottom of the pan to avoid leaking in the water bath

When you make a whole cotton cheesecake, you should prepare the parchment paper. Then grease the pan and the parchment paper with oil. In addition, dust powdered sugar over the parchment paper to rise the cheesecake smoothly in the oven. In the case of mini cheesecakes, all you have to do is line the muffin pan with cupcake liners.


It’s only required 6 ingredients:

  1. Cream cheese
  2. Eggs
  3. Sugar
  4. Cream (around 30 % fat)
  5. Flour (gluten free or other white flour)
  6. Lemon juice

Brief instructions

  1. Melt cream cheese with cream in a pan over a low heat.
  2. Once the cream cheese melted, transfer to a bowl and add sugar. Set aside to cool down.
  3. Beat egg whites until soft peaks. Set aside.
  4. Add egg yolks, lemon juice and flour to the cream cheese mixture and blend.
  5. Mix egg yolk mixture and egg white together.
  6. Pour the mixture into the liners and bake for 20 minutes in hot water bath.

I love to eat both when it’s warm and cold. When you eat them still warm, you can enjoy the super fluffy texture along with the fizzy and bubbly sounds in your mouth.

I brushed an apricot preserve on top. But also whipped cream and blueberry sauce would be nice to serve with the cheesecake.

If you would like to know more cheesecake recipe, check out my Japanese basque burnt cheesecake and cheesecake terrine!

Japanese cotton cheesecake cups gluten free
5 from 2 votes

Japanese Cotton Cheesecake Cups (GF)

Fluffy and jiggly Japanese cotton cheesecake cups made with a muffin pan. This mini souffle cake is quick and easy to make!
Author Matcha and Tofu
Servings: 12 cup cakes


  • 4 egg yolks
  • 4 egg whites
  • 200 g (7 oz) cream cheese
  • 200 ml (6.8 fl oz) Whipping cream / light cream or any cream around 30% fat
  • 8 tbsp (80 g) all purpose gluten free flour
  • 4 tbsp (60 g) granulated sugar for cream cheese
  • 3 tbsp (45 g) granulated sugar for egg whites
  • 1 tbsp lemon juice

Top coating (option)

  • 3 tbsp apricot preserve
  • 3 tbsp water


  • Preheat the oven to 140 C / 275 F / gas mark 1.
  • Line the muffin pan with 12 paper liners.
  • Melt the cream cheese with the whipping cream in a small pan over a low heat, whisking continuously.
  • Once the cream cheese melted and smooth, transfer to a bowl. Add the sugar (for cream cheese) and mix until sugar dissolved. Set aside to cool down.
  • Place the egg whites in a separate large bowl and beat with an electric whisk until foamy.
  • Add the sugar (for egg whites) in the egg whites and beat until soft peaks. (just before stiff peaks) Set aside.
  • Add the egg yolks to the cream cheese mixture one at a time and whisk after each addition.
  • Add the gluten free flour and whisk until well blended. Then add the lemon juice and mix.
  • Fold the 1/3 of the egg whites into the cream cheese mixture and blend with a hand whisk (not electric one) until well blended.
  • Fold the all cream cheese mixture into the rest of egg whites and gently blend with a rubber spatula until well combined and smooth.
  • Pour the mixture to the brim of the paper liners evenly and place on a oven tray.
  • Set the tray in the oven, then pour a few inch of hot water in the tray.
  • Bake for 20 minutes until a skewer inserted comes out clean.
  • Leave the cheesecake in the pan to cool down. Optionally, brush the mixture of apricot preserve and water on top of the cheesecake while cooling.
  • Enjoy your cheesecake, while it's warm or refrigerate them overnight and eat within 2 days.


I used a muffin pan with 4.5 cm (1.7 inch) diameter at bottom, 7 cm (2.7 inch) diameter at top, and 3 (1.2) cm height.

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Recipe Rating


Lea Stringer 1st 7月 2022 - 10:22 am

Yes, hello. My name is Lea, i am thinking about making this cheescake recipe. What would be better, all purpose or self rising flour? Thank you in advance for your reply.

momen 1st 7月 2022 - 10:53 am

Hi, Lea. Thank you for visiting my site. I haven’t use the both flour but self rising flour would be better to use for this fluffy cheesecake.

Tayler 17th 4月 2022 - 5:12 am

Hi! I’m trying this recipe now and I was wondering about the cooking temp!
I had mine @ 275 F for 20 minutes and it was still runny. Then I turned up the temp to 350 just to test it out, since I thought I ruined them LOL. but they puffed up in 3-4 minutes and started smelling good.
So im trying the second half of the batch at 325 or 350 to see if that works.

Wtye 9th 10月 2021 - 1:34 am

5 stars
Hi there! I would like to also ask if I can use regular plain flour?

momen 9th 10月 2021 - 7:08 am

Hi! Yes you can use plain flour!

Jessica 2nd 11月 2020 - 10:04 am

Hi I loved this recipe but had issues with the cooking time, are you supposed to put the muffin pan directly inside the oven pan with water ? Or keep both trays on separate racks ? I put my cheesecake muffin tray directly inside the pan and filled it with water but my bottoms were soggy and it took me a veryyy long time to cook to have the fork be cleaned . Thank you so much for clarifying !

momen 3rd 11月 2020 - 7:06 am

Hi, I put my muffin tin directly in the oven tray with hot water. In my case, the baking time was enough to be done. But I’ll check the baking time again. Thank you for your feedback!

Gigi Hofer 23rd 8月 2020 - 9:13 pm

Hi there. Sorry for bringing up this recipe after a year but I just chanced upon it now (fortunately!) and find it very interesting. I only have one question, for the gluten free flour, can I just use ordinary white rice flour? I am not familiar with using gluten free flours so forgive my ignorance. Thank you so much and I do hope to hear from you. Hioe you are well and good in these very strange and trying times we are in now.
Best regards,

momen 23rd 8月 2020 - 10:31 pm

Hi Gigi, I think that white rice flour is a good substitute for gluten free flour. I hope you enjoy the cheesecake. And also, please take care and stay healthy in this situation!