The tobamoviruses tomato brown rugose fruit virus (ToBRFV) and cucumber green mottle mosaic virus (CGMMV) have caused severe crop damages worldwide. Soil-mediated dispersion of the mechanically transmitted tobamoviruses constitute a major hindrance toward mitigating disease spread in crops carefully planted under sanitized conditions. Tobamoviruses are viable for months in soil and plant debris and for more than a year adhere to clay. However, a low percentage of infectious foci occur in soil following a tobamovirus-infected growing cycle, rendering disinfection studies of several contaminated plots inconclusive for large-scale crop productions. We have therefore formulated a rigorous platform for studying disinfectant efficacy in greenhouses by pouring a virus inoculum to planting pits prior to disinfectant treatment and by truncating seedling roots before planting, which was otherwise conducted under sanitized conditions. We have found that chlorine-based Taharan was significantly efficient in preventing disease spread of ToBRFV and CGMMV in tomato and cucumber plants, respectively. KlorBack was often as good as Taharan. In addition, a formulation of chlorinated tri-sodium phosphate used at a nonphytotoxic 3% concentration showed disinfection efficiency similar to Taharan effect on ToBRFV infection only. Our study provided a small-scale platform for disinfectant efficacy evaluation necessary for application in tobamovirus-contaminated soil, which commonly occurs in commercial tomato and cucumber greenhouses.