The choice of miso paste for the miso soup defines a great deal of its character and flavor. Miso pastes (a traditional Japanese seasoning produced by fermenting soybeans with salt and the fungus Aspergillus oryzae, known in Japanese as kōjikin (麹菌?), and sometimes rice, barley, or other ingredients) can be categorized into red (akamiso), white (shiromiso), or mixed (awase). There are many variations within these themes, including regional variations, such as Shinshū miso or Sendai miso.
A miso paste that has been fermented for a longer period of time, such as a red miso, gives the miso soup a stronger, deeper flavor. A miso paste that has been fermented for a shorter period of time, such as a white miso, provides a lighter, sweeter flavor.
More than 80% of Japan's total annual production of miso goes into miso soup, and 75% of all Japanese consume miso soup at least once a day.
The most common dashi soup stocks for miso soup are made of niboshi (dried baby sardines), kombu (dried kelp), katsuobushi (thin shavings of dried and smoked bonito, aka skipjack tuna), or hoshi-shiitake (dried shiitake). The kombu can also be used in combination with katsuobushi or hoshi-shiitake. The kelp and/or shiitake dashi serve as a vegetarian soup stock.
Outside Japan, American or European style miso soup is sometimes made by dissolving miso in a Western vegetable stock. The stock might include ingredients such as negi, carrot, potato and daikon radish. In some versions of the dish chicken stock, Western-style fish stock, and other non-dashi bases can even be used, but there is some debate over whether or not miso soups made using these non-traditional bases count as true misoshiru. Christian Japanese refugees who came to the Philippines during the Edo period brought along miso soup, but the Filipino recipe sinigang differs mainly by the inclusion of tamarind, which gives it a more sour taste than the original Japanese version.
According to Japanese custom, the solid ingredients are chosen to reflect the seasons and to provide contrasts of color, texture, and flavor. Thus negi and tofu, a strongly flavored ingredient mixed with a delicately flavored ingredient, are often combined. Ingredients that float, such as wakame seaweed, and ingredients that sink, such as potatoes, are also combined. Ingredients may include mushrooms, potatoes, seaweed, onion, shrimp, fish, clams, and sliced daikon. Nearly any Japanese ingredient is added to some type of misoshiru. However, misoshiru does not typically contain many ingredients beyond the stock and miso.
If pork is added to miso soup, it is called tonjiru, meaning "pork soup".
Miso soup can be prepared in several ways, depending on the chef and the style of soup. Japanese recipes usually call for most vegetables and meats to be cooked in the simmering dashi, particularly mushrooms, daikon, carrots, potatoes, tofu, and fish. The miso is suspended separately in some dashi stock removed from the simmering mix, to keep the miso paste from cooking, which alters the flavour, kills beneficial bacteria, and reduces the health benefits of biologically active miso paste. When the vegetables are cooked, the stock is removed from heat, the miso suspension is added and mixed into the soup, any uncooked ingredients are added, and the dish is served.
In Japan, miso soup and white rice make up the central dishes of the traditional Japanese breakfast. The soup has been a favorite of commoners and royalty alike for many centuries, but there are also many other dishes involving breakfast. They are all quite small, some include egg, fish, and nattō which is a fermented soy bean. The soup is usually served in lacquer bowls with lids and drunk directly from the bowl, though the solid ingredients are eaten with chopsticks. The bowl sometimes has a lid to keep heat and aroma in as well as to improve the presentation.
Instant miso soup is available in single-serving packets. It is sold in dehydrated powder and paste forms. It generally contains dried toppings such as wakame and tofu with soy beans that reconstitute rapidly on the addition of hot water. These are popular in the Japanese workplace, where miso soup can be made with lunch as easily as green tea and using the same water. Instant miso soup is available in many grocery stores outside Japan. It has a shelf life of 3 to 12 months.
Wappani (wappani (わっぱ煮)) is a miso-soup-based dish unique to Awashima island off the coast of Niigata, Japan. A cedar flask ("wappa") is filled with miso soup, fish and vegetables and it is heated by dropping in hot rocks, which quickly bring it to a simmer. Hot rocks retain their heat for hours after being taken from the fire, so a hot meal can be prepared without the use of fire.
In 2003, researchers at Japan's National Cancer Centre suggested that "eating three or more bowls of the Japanese delicacy Miso soup every day could cut women's risk of developing breast cancer". Miso soups also tend to be low in calories, but are filling because of the high protein content.