An innovative biodegradable bio-based packaging system has been designed to achieve Equilibrium Modified Atmosphere Packaging (EMAP) of high value fresh horticultural produce through optimised barrier properties obtained by laser micro-perforations combined with selectively permeable membrane technologies. Polylactic Acid (PLA) film was used as packaging material replacing conventional biaxial oriented polypropylene (BOPP) films. The tested commodities were fresh cherry tomatoes and peaches. The micro-perforated PLA EMAP packages appear to perform very well for both commodities due to their higher water vapour permeability compared to conventional materials. 3D numerical simulations were employed as a tool to design and analyse the performance of the novel EMAP system. The numerical simulations results were found to be in good agreement with the experimental data, with the average values differences being within the standard deviations (<5%). The numerical results were also found to agree with the average values predicted by an analytical model. The computational analysis provided detailed 3D mapping of the gas mixture concentrations in the EMAP headspace. 3D mapping not only confirmed the experimental average data but also identified dysfunctional packaging details and explained fruit skin deformations and regions of water vapour condensation observed in conventional BOPP EMAP.