In the Japanese agricultural industry, efforts are being made to recycle waste produced in order to use resources more efficiently. However, in some cases, when stored for long periods of time these materials generate heat through fermentation, which can eventually result in spontaneous ignition or oxygen deficiency in storage areas, resulting in the deaths of workers. In this study, we conducted a series of experiments on several types of agricultural waste (organic waste generated by agricultural production activities in Japan) frequently stored for recycling, using combinations of various thermal- and gas-analysers, in order to identify the risk factors related to spontaneous ignition and oxygen deficiency accidents. The aim of this research was to understand the circumstances leading to spontaneous ignition and oxygen deficiency accidents in storage facilities and to recommend safety measures to prevent such occurrences. Our results suggest that fermentation is likely responsible for the generation of heat and production of carbon dioxide at temperatures up to approximately 50 °C, where microbial activity diminishes. At temperatures beyond 50 °C, a transition into heat generation by the oxidation of fatty acid esters occurs. Additionally, when the barrier of heat absorption is overcome at around 100 °C due to the evaporation of water, there is a transition to thermal cracking that could lead to fire. Accidents due to oxygen deficiency may occur when a storage facility is well sealed and the amount of oxygen circulation is minimal. However, when the amount of oxygen is sufficient; the substance is stored in large deposits; and the facility is well insulated, fermentation can cause the temperature to increase. Therefore, it is desirable to periodically measure the temperature of stored materials and monitor the generated gases.