The Brazilian Agricultural Research Agency (Embrapa) has proposed a “System for Environmental Impact Assessment of Agricultural Technology Innovations” (Ambitec-Agro) for the appraisal of research projects and technology innovations in the institutional context of R&D. A derived system, directed at eco-certification of rural activities (Eco-cert.Rural), has been proposed in order to extend the environmental assessment practice to rural activities. The Ambitec-Agro System comprises a set of weighing matrices organized for the integrated assessment of socio-environmental indicators, including modules focused on the environmental impact assessment of Agricultural, Livestock production, and Agro-industrial activities and a specific module for Social Impact Assessment. The calculated impact indices facilitate socio-environmentally sound decision making and allow the delineation of ad hoc recommendations for performance improvements, as well as selection of best cases for benchmarking purposes. The paper presents the Ambitec-Agro System and its applications as a project appraisal and technology management methodology.