Nature is a source of biologically active products that can act as fungicides, bactericides, acaricides, herbicides and insecticides. However, the application of these biopesticides can be challenging because they are generally insoluble in aqueous phases, highly volatile and unstable. One strategy to promote their use is their encapsulation into natural hosts, cyclodextrins. Cyclodextrins are food-grade and readily biodegradable oligosaccharides obtained from the enzymatic degradation of starch. Encapsulation in cyclodextrins would offer many advantages such as increased solubility, lower release rates and protection against chemical and physical degradation. Herein, we review the efficacy of cyclodextrin/natural compound inclusion complexes for crop protection. We discuss preharvest treatment and the different stages of the postharvest handling such as storage, distribution, packaging and marketing.