Plant pathogenic fungi are the most important cause of losses in agriculture. In the context of the overuse of synthetic fungicides, natural products are an encouraging alternative to control these plant pathogenic fungi. In this study, we tested the antifungal capacity of four strains of the genus Streptomyces against the plant pathogenic fungi Alternaria alternata, Botrytis cinerea and Fusarium oxysporum. We also investigated the effect of applying the extracts with the highest antifungal activities in a post-harvest setting for the control of B. cinerea on cherry tomato fruits. The results revealed the ability of these strains, especially Streptomyces netropsis A52M, to inhibit in vitro the growth and, in some cases, the sporulation of plant pathogenic fungi. The protective effect of the S. netropsis A52M extracts on post-harvest cherry tomato fruits infected with B. cinerea was demonstrated. In addition, when grown in co-culture, we observed an interesting phenomenon in which the Streptomyces mycelium physically encapsulated the fungal mycelium, contributing to its inhibition. This outcome offers the potential for research into the role of physical microbial interactions in fungal biocontrol. To sum up, the findings outlined here for the interactions between Streptomyces strains and plant pathogenic fungi are a promising, safer, and more sustainable biocontrol alternative to chemicals for agriculture. This is of particular interest in the protection of perishable agricultural products during the post-harvest phase.