Postharvest microbial spoilage due to suboptimal transportation and packaging conditions is a key concern for the South African tomato industry. This study investigated the influence of washing with tap water or aqueous disinfectant solutions (chlorinated and anolyte water) on the microbiological quality of tomatoes during storage after transportation in nonrefrigerated trucks along two supply routes when packaged in crates and boxes. Route 1 was 1,093 km from field to storage site, while route 2 was 1,057 km. During transport, the temperature in the trucks fluctuated between 16 and 28°C and the relative humidity between 25 and 94% for route 1, while for route 2, the temperature was between 16 and 30°C and the relative humidity between 28 and 71%. Tomatoes at the pink maturity stage were sampled, treated, and stored for 28 days (11°C). The tomato firmness before treatment was 24.8 N (box samples) and 17.4 N (crate samples) for route 1, whereas it was 22.1 N (box samples) and 20.2 N (crate samples) for route 2. Temperature fluctuation during transportation led to water condensation on tomato surfaces. Tomatoes treated with anolyte water showed the lowest microbial surface burden during storage, with mean aerobic plate counts (APC) of 2.9 log CFU/cm2, coliform counts (CC) of 1.1 log CFU/cm2, and fungal counts (FC) of 2.3 log CFU/cm2. Overall, of the total APC recorded during storage, anolyte-treated samples contributed 9% while chlorinated water-treated samples contributed 30%. Of the total CC, anolyte samples presented 3% while chlorinated water samples made up 12%, and of the total recorded FC, anolyte samples contributed 7% while chlorinated water samples made up 22%. Scanning electron microscopy imaging showed surface cracks, which enable microbial colonization in crate-transported tomatoes. A combination of anolyte treatment and box packaging during transport resulted in the best microbiological quality during storage. The findings of this investigation provide motivation for the adoption of anolyte water as a postharvest disinfection treatment in the tomato industry.