The article analyzes the physical, chemical, and biological changes occurring during the storage of raw cotton. The distribution of moisture and temperature within cotton piles, as well as the influence of microbiological activity and oxidation reactions on fiber quality, are discussed in detail. A physical model of the self-heating process in cotton storage piles has been developed, and practical recommendations are proposed for implementing a mechatronic microclimate control system to prevent self-heating and ensure fiber preservation.