The United States is the world's largest producer of blueberries and strawberries. Successful marketing for both of them requires fruit of the highest quality and appearance. However, these fruits have a relatively short postharvest life, mostly due to the incidence of molds such as Colletrotrichum acutatum, Alternaria alternata, and Botrytis cinerea. At present, several natural occurring plant volatiles have been shown to be effective against fungal growth, but, even so, those compounds could not be maintained at constant concentration during the whole postharvest period due to their volatility. In this work, two naturally occurring aldehydes (acetaldehyde and hexanal) were tested and compared against the growth of the above mentioned fungi at 23 °C. After that, the most effective antifungal compound for each fungus was encapsulated in ß-cyclodextrins (ß-CD) and tested during storage period. Both aldehydes were effective in reducing and avoiding fungal proliferation depending on concentration. Fungal proliferation depended on daily, and not initial, volatile concentrations. Volatiles encapsulated in ß-CD showed higher antifungal activity compared to that obtained using the pure volatile during storage. Tested volatiles showed both fungicidal and fungistatic capacities after storage of fungal cultures in air. Results suggested ß-CD-acetaldehyde and ß-CD-hexanal complexes can be used as a new technology to release a naturally occurring antifungal compound during storage against several fungal diseases.