The present work aimed to investigate the self-heating process of agricultural residues during storage and to evaluate its impact on the properties of the stored fuels. Two types of biomass, rice straw and husk, were used as raw materials. Their self-heating processes and characteristics were investigated by storing the materials with different moisture contents and particle sizes in a bench-scale reactor and monitoring the evolution of inside temperatures. The resulting materials were systematically characterized. Comparison of the composition, calorific value, pH value, surface structure, and combustion characteristics between the initial and stored materials were performed to assess the influence of moderate self-heating on the fuel properties. Observations on the evolution of the temperatures inside stored materials showed that the characteristics of the self-heating process including the induction time, period with significant heat generation, and peak temperature as well as the hottest position within the sample depend upon biomass type, initial moisture content, and particle size of the sample. Characterization of fuel properties showed that moderate self-heating during storage slightly changed the proximate composition of dry biomass but resulted in considerable losses of dry matter and energy as well as a slight increase in the fuel combustion reactivity. The higher moisture contents and smaller particle size benefit self-heating. Rice straw is more prone to self-heating than rice husk under the same conditions, as reflected by the higher extent of the self-heating and the more dry matter and energy losses.