[10] Murdijati Gardjito, a food historian at Gadjah Mada University, argued that tempeh was made by native Javanese people and that its preparation predates the introduction of Chinese-style tofu products.

Mary Astuti, a food historian at Gadjah Mada University specializing in tempeh, argued that the native variety of soybean had been grown before the Chinese arrived in the region.

By the 16th or the 19th century, depending on which period of time the writer of Serat Centhini referred to, Javanese people had mastered the art of cooking with tempeh, when it was not only eaten as is, but converted into different types of dishes, showing a full understanding and mastery of the food product.

[11] Gardjito noted that Javanese noble families rarely wrote about tempeh in ancient texts because it had never been a part of royal cuisine, but rather a staple food of the lower classes.

supported this idea, saying that tempeh might have been accidentally produced as the by-product of the tofu industry in Java in the 17th century, as discarded soybeans caught the spores of a whitish fungus that was found to be edible.

The original version of tempe dhele has been forgotten as tahu has become the common people's food, and dependence on imported white soybeans grows.

[13] Adding vinegar during soybeans soaking process had also been reported in tempeh industries and it had been found to influence the sensory nature of the final product.

Under conditions of lower temperature, or higher ventilation, gray or black patches of spores may form on the surface—this is not harmful, and should not affect the flavor or quality of the tempeh.

The undersides of the leaves are covered in downy hairs (known technically as trichomes) to which the mold Rhizopus oligosporus can be found adhering in the wild.

This results in white woolly appearance and more pleasant aroma compared with tempeh made with commercial starter containing only Rhizopus oligosporus.

[21] During the processing of soybeans to make tempeh there are inevitable losses of material due to the removal of the hulls and the leaching of soluble compounds during the soaking, washing and cooking stages.

Inedible tempeh has beans with foul odor, resembling strong ammonia or alcohol, indicating the development of undesirable bacteria due to excess moisture or overheating.

[25] Tempeh is a perishable food and must be wrapped and placed into the refrigerator or freezer immediately after incubation or other processing steps such as blanching.

[30] In western countries, it is more common to use a pure culture containing only Rhizopus oligosporus, which makes little B12 and could be missing Citrobacter freundii and Klebsiella pneumoniae, which have been shown to produce significant levels of B12 analogs in tempeh when present.

In Java, tempeh is often traditionally prepared by cutting it into pieces, marinating it in a mixture of ground garlic, coriander, turmeric, salt and water; then deep fried,[33] and it's often served with sambal ulek chili paste.

Sometimes when tempeh is diced and left, it will create white feathery fluff which bonds the cut—this is the Rhizopus mold still growing—this is normal and perfectly edible.

A related product to tempeh is oncom, which is made from peanut press cake or soy dregs and is prevalent in Sundanese culture in West Java.

According to traditional Javanese customs, wasting food is deemed as a sign of disrespect to Nature and other beings, and encourages efforts to use every part of an ingredient.

Having a slightly pungent aroma, small amounts are used as a flavoring agent in traditional Javanese sayur lodeh vegetable stew and sambal tumpang.

This type of tempeh served as a main source of protein in Java due to its inexpensiveness and has led to several cases of fatal food poisoning,[42] as it occasionally gets contaminated with the bacterium Burkholderia gladioli, and the unwanted organism produces toxins (bongkrek acid and toxoflavin) from the coconut, besides killing off the Rhizopus fungus due to the antibiotic activity of bongkrek acid.

[43] During 1930s, Indonesian government went through an economic depression, and this condition caused some of the people to make tempe bongkrek by themselves, instead of buying it directly from well-trained producers.

Dutch scientists W. K. Mertens and A. G. van Veen from the Eijkman Institute of Jakarta, started to find the cause of the poisoning in the early 1930s.

B. cocovenenans is commonly found in plants and soil, which can be taken up by coconuts and corn, leading to the synthesis of bongkrek acid during the fermentation of such foods.

The tempeh is sliced and seasoned in a mixture of ground garlic, coriander seeds and salt, and then deep fried in palm oil.

Bacem is a Javanese cooking method of braising in spices and palm sugar and boiling the food in a closed place until the water runs out.

[50] The tempeh is first braised in a mixture of coconut water, palm sugar, and spices including coriander seeds, shallots, galangal, and bay leaves, and then briefly deep-fried.

The tempeh is first dipped in spiced flour before quickly frying in very hot oil, resulting in a product that is cooked on the outside, but raw or only partially so on the inside.

[52] The raw tempeh is cut into small sticks and thoroughly deep-fried until no longer moist, and then mixed with palm sugar, chili pepper or other spices, or with sweet soy sauce.

[58] Fried, grilled or otherwise cooked tempeh patties, sandwiched between slices of bread or hamburger buns with salad, sauces or seasonings.

Storage life could be extended to two or three weeks if the tempeh is blanched or steamed prior to refrigeration due to the inactivation of enzymes and destruction of bacteria.