In this study, the ability of multilayer nanocomposite films based on low density polyethylene (LDPE) containing organic layered double hydroxides (OLDH) and volatile thyme oil (TO) bioactives is explored as a non-traditional treatment method for post-harvest disease control in ‘Hass’ cultivar of avocados. Transparent flexible trilayer films were made using single step blown film extrusion using varying concentrations of OLDH and 5 wt% of TO. The optical, mechanical and barrier properties of the films were studied to substantiate the film functionality. The active packaging film containing TO and 2 wt% OLDH showed considerable reduction in anthracnose disease events in avocados in comparison to commercial treatment and untreated control. In addition, the active multilayer film with optimal clay loading showed improved oxygen and moisture barrier properties without affecting its transparency and flexibility. The results suggest that the synergistic effect of antimicrobial properties arising from volatile bioactive release and barrier properties of the composite films can be utilised as a prospective strategy to create modified atmosphere thereby improving shelf life and quality of avocados.