The aim of this study was to examine the current coffee production and processing system in Costa Rica in order to maximize its sustainability through cost and risk reductions and identification of new opportunities. A two-year field investigation was performed for assessing resource, energy and water uses, characterizing by-products, and evaluating training, management and industry structure, with the aim of identifying opportunities for the implementation of Cleaner Production (CP) and industrial ecology (IE) strategies. The application of industrial ecology has been implemented in a piecemeal fashion and has not, therefore, been widely accepted by the industry at large. The broader coffee production system in Costa Rica does not encourage the practice of environmentally sustainable methods within production or processing, and does not encourage the exploration of niche markets that reward high-valued coffee in terms of quality or socio-environmental consciousness. Changes in industrial throughput, operational design, and management attitudes are needed to ensure sustainability within the industry. A number of opportunities for maximizing the sustainability of the coffee industry exist through: (a) strategic application of Cleaner Production, (b) effective use of resources, (c) alternative use of by-products, (d) efficient operational design, (e) training, (f) introduction of basic environmental management concepts, and (g) changes to industry structure. The paucity of data regarding research into the specific barriers to innovations within the coffee industry requires investigation. The specific barriers to the application of environmental innovations need to be identified and understood. This must include the social, cultural and institutional aspects governing the industry in addition to the technical and economic aspects normally addressed.