The control of micro-organisms responsible for pre- and postharvest diseases of agricultural products, mainly viruses and fungi, is a problem that remains unresolved, together with the environmental impact of the excessive use of chemicals to tackle this problem. Current efforts are focused on the search for efficient alternatives for microbial control that will not result in damage to the environment or an imbalance in the existing biota. One alternative is the use of natural antimicrobial compounds such as chitosan, a linear cationic biopolymer, which is biodegradable, biocompatible and non-toxic, has filmogenic properties and is capable of forming matrices for the transport of active substances. The study of chitosan has attracted great interest owing to its ability to form complexes or matrices for the controlled release of active compounds such as micro- and nanoparticles, which, together with the biological properties of chitosan, has allowed a major breakthrough in the pharmaceutical and biomedical industries. Another important field of study is the development of chitosan-based matrices for the controlled release of active compounds in areas such as agriculture and food for the control of viruses, bacteria and fungi, which is one of the least exploited areas and holds much promise for future research.