In the fridge of course! :)

You can buy a fridge from the premium section in your decoration menu and place it in your cafe. Once you have a fridge, you can tap on dishes that are on the counter and store them in the fridge. This helps keeping the dishes fresh and giving you extra space for preparing/serving more dishes!

You can also increase the capacity of your fridge to store more food! Currently the maximum storing capacity is 80000 servings.