Background In a previous study, a lactic acid bacterium, Enterococcus faecium, was locally isolated from Egyptian soil and its ability to inhibit the growth of a test phytopathogen was proven. Objective The study was performed to assess the ability of the tested strain to grow on different media. The produced antifungal agent was investigated. Finally, the strain was encapsulated within different biopolymers to increase its viability. Materials and methods Several byproducts were tested and compared with the standard De Man-Rogosa-Sharpe medium. The antifungal activity was tested using the poisoned food technique. Chromatographic analysis of the fermentation medium was performed using high-performance liquid chromatography. Production of chitinase was confirmed by cultivating the test strain on chitin and estimating the amount of reducing sugars using the Somogyi method. The E. faecium cells were also encapsulated within soy protein isolate-alginate beads, gellan gum discs, and carboxymethyl cellulose beads. Results and conclusion The strain was able to grow on all of the tested byproducts and exerted a potent antifungal activity against Fusarium solani, especially when a very economic medium, mainly composed of whey, was used. High-performance liquid chromatography results confirmed the production of a number of organic acids that contributed in the inhibition of the fungal growth. The study also proved the production of chitinase enzymes, which apparently altered the chitinous layer present in the cell wall of F. solani, causing disintegration of the fungal cells. It was also shown that encapsulation of E. faecium increased its viability in soil as compared with the free uncapsulated strain.