In‐package sanitisation was developed using polylactic acid (PLA) films with allyl isothiocyanate (AIT) vapour. Tomatoes were artificially inoculated with Escherichia coli, Geotrichum candidum and Fusarium oxysporum and stored in clamshell boxes with the film fixed to the underside of the lid. The changes in bacterial and fungal populations and the quality of tomatoes during storage at 4 and 10 °C were evaluated. The results revealed that the film treatment (4 × 8 cm2 film in 1 L box) reduced the populations of inoculated bacteria and fungi on tomatoes by 2–3 log CFU g−1, and then significantly (P < 0.05) inhibited their growth during the 21‐day storage period at both temperatures. Tomatoes subject to film treatment had fewer changes in quality (colour, firmness, contents of total soluble solid, titratable acids and vitamin C) than the control samples during storage. The antimicrobial PLA film can be used for in‐package sanitisation to extend the shelf‐life of packaged tomatoes or similar perishable vegetables.