Storage of bulk biomass materials is essential along the feedstock supply chain of bioenergy production. The self-heating accompanying biomass storage has hazardous consequences. With the increasing biomass utilization for bioenergy production, the risk and economic and environmental concerns about biomass storage have been attracting extensive research attention aimed at understanding the processes of heat generation, evaluating the propensity of a material to self-heating and spontaneous ignition, describing and predicting the self-heating process and consequences in biomass storage, and developing strategies and technologies for storage management. The advances in the understanding and description of heat generation processes including water-associated physical processes, microbiological degradation processes, and chemical oxidative processes during the self-heating in biomass storage are reviewed, with the focus on understanding the processes and their underlying mechanisms, reaction kinetics, and heats of reaction through experimental studies and description of heat generation and self-heating processes through kinetic analyses and modeling. This review highlights the need to improve the mechanistic model description of the self-heating processes and associated material changes and product formation, which demand a better understanding and description of microbial degradation and chemical oxidation through experimental study.