The European directive 2008/98/CE establishes a legal framework for the treatment of waste within the Community. It aims at protecting the environment and human health through the prevention of the harmful effects of waste generation and waste management. In order to better protect the environment, the Member States should adopt measures for the treatment of their waste according to a hierarchy as outlined: prevention, preparing for reuse, recycling, energy recovery, disposal. In this context, the European project LIFE12 ENV/IT/000356 “RESAFE” is addressed to produce and utilize a new class of fertilizers characterized by reduced salinity in order to substitute chemical and mineral fertilizers through a technological route based on Urban Organic Waste (UOW), Farm Organic Residues (FOR), Bio-Chars (BC) and Vegetable Active Principles (VAP) processing. Following this approach, it will be possible for farmers and urban waste managers to reduce costs and to obtain environmental and economic incomes. Furthermore, environmental impacts will be also reduced contributing to decrease the greenhouse emissions from landfills and from the production of mineral fertilizers. In this paper, specific innovative sensing architectures, based on Hyper-Spectral Imaging (HSI) devices working in the near infrared (NIR) range, and related detection architectures, is presented and discussed in order to define and apply smart detection engines to follow the transformations of the complex material, resulting from UOW, FOR, BC and VAP based recipes during the different stages of the fertilizer production process. Results show as the fertilizer production process can be monitored adopting the NIR-HSI approach.