The importance of environmentally-friendly electricity production is recognized as one of the most important challenges of our future, covering a broad context of research topics and promoting future scenarios based on renewable energies and new technologies. In the short term, however, energy generation will still be largely relying on power plants fired with fossil fuels whose emissions of pollutants are regulated by the industrial emissions directive in the EU legislation. Such directive does not apply to small and medium combustion plants, which until now, have only been subject to national regulations. As part of its air quality package from December 2013, the EU Commission has proposed a new directive which forces such plants to provide periodic measurements of pollutants, keep records of their environmental impact and provide information to the competent authorities. This situation has renewed the attention towards the systems for continuous emission monitoring in SMC. Such systems are in fact very expensive, therefore they require an optimized design in order be affordable for a SMC. This research, in particular, refers to the context of micro-grids and isolated power generation plants based on a set of diesel engine generators (GenSet) and addresses the topic of the development decision support systems (DSS) for environmentally-friendly power genset management. The system is based on a Selective Catalytic Reduction (SCR) reactor coupled with continuous emission monitoring system (CEMS) to reduce the environmental impact and generate information to support the management processes. The paper also reports the preliminary experimental results obtained in the power plant located in the small island of Favignana in the Mediterranean sea. These results demonstrate how the system developed and the approach proposed reduces the emission of pollutants with a substantial benefit for the local community, in a context where more environmentally efficient production technologies can hardly be employed