To design new packaging for fresh food, stakeholders of the food chain express their needs and requirements, according to some goals and objectives. These requirements can be gathered into two groups: (i) fresh food related characteristics and (ii) packaging intrinsic characteristics. Modified Atmosphere Packaging (MAP) is an efficient way to delay senescence and spoilage and thus to extend the very short shelf life of respiring products such as fresh fruits and vegetables. Consequently, packaging O2/CO2 permeabilities must fit the requirements of fresh fruits and vegetable as predicted by virtual MAP simulating tools. Beyond gas permeabilities, the choice of a packaging material for fresh produce includes numerous other factors such as the cost, availability, potential contaminants of raw materials, process ability, waste management constraints, etc. For instance, the user may have the following multi-criteria query for his/her product asking for a packaging with optimal gas permeabilities that guarantee product quality and optionally a transparent packaging material made from renewable resources with a cost for raw material less than 3 e/ kg. To help stakeholders taking a rational decision based on the expressed needs, a new multi-criteria Decision Support System (DSS) for designing biodegradable packaging for fresh produce has been built. In this paper we present the functional specification, the software architecture and the implementation of the developed tool. This tool includes (i) a MAP simulation module combining mass transfer models and respiration of the food, (ii) a multi-criteria flexible querying module which handles imprecise, uncertain and missing data stored in the database. We detail its operational functioning through a real life case study to determine the most satisfactory materials for apricots packaging.