Muscodor is an endophytic fungal genus whose members produce volatile organic compounds (VOCs) with broad antimicrobial, nematocidal and insecticidal activities. This study describes the isolation and characterization of a new strain of Muscodor albus, designated as M. albus aa3, from wild pineapple (Ananas ananassoides) plants collected in Havana, Cuba. In vitro cultures of M. albus aa3 on both potato dextrose agar media (PDA) and paddy produced VOCs with antimicrobial activity against Escherichia coli and plant pathogens, including several species of the Phytophthora genus and the wood rot fungus Fomitiporia maxonii; but innocuous to the beneficial mycopathogen Trichoderma koningii. GC/MS analysis indicated the unique composition of the mixture of VOCs emitted by aa3, in which sesquiterpenes represent the most abundant compounds. VOCs emitted during the growth of M. albus aa3 on paddy grains protected Persian lime (Citrus × latifolia Tanaka) fruits from infection by Phytophthora nicotianae Breda de Haan, suggesting the potential use of this fungus for postharvest biofumigation. Isolation of M. albus from wild pineapple points out this plant as a susceptible host to be colonized by distinct species of the Muscodor genus.