Sustainability assessment is a mainstream business activity that demonstrates the link between the organization’s strategy for and commitment to a sustainable global economy, and the prevention of economic crises. Small- and medium-sized businesses/enterprises (SMBs/SMEs) have significant effects on the European economy. However, because of a lot of restriction factors, like business risk, the high expenses of data collection and management, and the lack of resources, sustainability reporting is considered a superfluous and burdensome activity for them. The aim of this research is to propose an automated, comprehensive and simplified system for the sustainability assessment of SMEs. This system is achieved by implementing three main phases. The first phase includes key performance indicators design, which starts with the identification of various key performance indicators for comprehensive sustainability assessment, and ends with proposing an optimal set of KPIs (Key Performance Indicators) that can encompass long-term issues and be applicable to SMEs in the EU. The second phase involves a new comprehensive method of sustainability assessment for all KPIs designed in the first phase. Therefore, a multi-criteria model, which involves four main pillars of sustainability assessment (economic, environmental, social and governance), is proposed. It gives different enterprises the ability to verify and compare their efficiency and sustainability with other companies within the same sector in an almost automated manner. In the final phase, a simple and an automated information system (WEBRIS), which provides a suitable environment for SME sustainability reporting, is developed. Finally, this system is verified in a case study of the Czech breweries sector.