This chapter examines the relationship between cereal grains during storage and approaches which have been used to minimise fungal spoilage and mycotoxin contamination. The role of abiotic factors such as water availability and temperature and their interactions on ecology of spoilage and mycotoxigenic fungi are discussed. The use of volatile organic compounds (VOCs) as an early indicator of spoilage is also reviewed. The potential for the early detection of initiation of fungal spoilage moulds in stored grain by using CO2 as an early warning is examined in combination with predictive modelling of boundary conditions for growth and toxin production as tools for the development of DSS systems. Control measures including abiotic factors, use of natural preservatives, biocontrol agents, and physical methods such as irradiation, cold plasma treatments, hermetic bag systems and fumigation with ozone (O3) are considered. Finally, the potential of developing real time approaches for better post-harvest management of stored cereals and other commodities are discussed.