The efficacy of traditional control measures for the management of plant pathogens is decreasing, and the resistance of these pathogens to pesticides is increasing, which poses a serious threat to global food security. The exploration of novel and efficient management measures to combat plant disease is an urgent need at this time. In this study, fungal metabolites from three Trichoderma spp. (T. harzianum, T. virens and T. koningii) were prepared on three different growth media (STP, MOF and supermalt (SuM)). The fungal metabolites were tested in vitro and in vivo from March–April 2020 under greenhouse conditions in a pot experiment utilizing completely randomized design to test their management of the bacterial wilt disease caused by R. solanacearum in tomato plants. The effect of the fungal metabolites on bacterial cell morphology was also investigated through scanning electron microscopy (SEM) analysis. In vitro investigation showed that the fungal metabolites of T. harzianum obtained on the STP medium were the most effective in inhibiting in vitro bacterial growth and produced a 17.6 mm growth inhibition zone. SEM analysis confirms the rupture of the cell walls and cell membranes of the bacterium, along with the leakage of its cell contents. Generally, fungal metabolites obtained on an STP medium showed higher activity than those obtained on the other two media, and these metabolites were then evaluated in vivo according to three application times (0 days before transplantation (DBT), 4 DBT and 8 DBT) in a greenhouse trial to examine their ability to manage R. solanacearum in tomato plants. Consistent with in vitro results, the results from the greenhouse studies showed a level of higher anti-bacterial activity of T. harzianum metabolites than they did for the metabolites of other fungi, while among the three application times, the longest time (8 DBT) was more effective in controlling bacterial wilt disease in tomato plants. Metabolites of T. harzianum applied at 8 DBT caused the maximum decrease in soil bacterial population (1.526 log cfu/g), resulting in the lowest level of disease severity (area under disease progressive curve (AUDPC) value: 400), and maximum plant freshness (with a resulting biomass of 36.7 g, a root length of 18.3 cm and a plant height of 33.0 cm). It can be concluded that T. harzianum metabolites obtained on an STP medium, when applied after 8 DBT, can suppress soil bacterial population and enhance plant growth, and thus can be used as a safe, environmentally-conscious and consumer-friendly approach to managing bacterial wilt disease in tomato plants and possibly other crops.