This study aimed to examine the total viable bacteria (TVBC); total coliform (TCC); fecal coliform (TFC); pathogenic Pseudomonas spp., Staphylococcus aureus, and total fungi (TF); and the effect of different low-cost disinfectants (sterile water, salt water, blanched, and vinegar) in decontamination of 12 types of fruit and 10 types of vegetables. In fruit samples, the lowest TVBC was enumerated at 3.18 ± 0.27 log CFU/g in Indian gooseberry and the highest at 6.47 ± 0.68 log CFU/g in guava. Staphylococci (2.04 ± 0.53–5.10 ± 0.02 log CFU/g), Pseudomonas (1.88 ± 0.03–5.38 ± 0.08 log CFU/g), and total fungi (2.60 ± 0.18–7.50 ± 0.15 log CFU/g) were found in all fruit samples; however, no Salmonella was detected in fruit samples. Similarly, the lowest TVBC recorded 5.67± 0.49 log CFU/g in cucumber and the highest 7.37 ± 0.06 log CFU/g in yard long bean. The Staphylococci (3.48 ± 0.13–4.81 ± 0.16 log CFU/g), Pseudomonas (3.57± 0.21– 4.75 ± 0.23 log CFU/g), TCC (1.85 ± 1.11–56.50 ± 37.14 MPN/g), TFC (1.76 ± 0.87– 3.78 ± 3.76 MPN/g), and TF (3.79 ± 0.18–4.40 ± 0.38 log CFU/g) were recorded in all vegetables samples, but no Salmonella was detected in yard long bean, pointed gourd, carrot, tomato, cucumber, or brinjal. However, vinegar showed the highest microbial load reduction of selected fruit and vegetables among the different treatments. With vinegar treatment, the highest reduction of TVBC (1.61-log) and TF (2.54-log) was observed for fruits, and TVBC (2.31-log) and TF (2.41-log) for vegetables. All the disinfectant treatments resulted in significant (p < 0.01) bacterial load reduction compared to control for the studied fruits and vegetable samples.