The European sheep and goat sector is characterized by low professionalization and management training. Moreover, it is fragmented in terms of production aims and farming systems. Here, iSAGEDSS, a web-based application allowing dairy and meat small ruminant farmers in different countries to make annual management plans by testing future scenarios, is presented. Data were obtained for the meat sheep (United Kingdom and Spain), dairy sheep (France and Greece) and dairy goat production systems (Greece) from partners of the Innovation for Sustainable Sheep and Goat Production in Europe (iSAGE) project. These were used to set default values and ranges for all important farm parameters in each system and country. An algorithm was developed assessing nutritional management and its impact on production and financial performance. Reports focus on profitability, productivity and environmental sustainability. A case study in three dairy sheep farms in Greece was performed. In each case, an evaluation scenario was created using actual farm data that were compared with the estimated ones. Two scenarios testing management decisions for gross margin maximization and milk pricing fluctuations were created. Application results showed high prediction accuracy for gross margin and production estimation (error of circa 9% and 4%, respectively). Moreover, the ability to promote financial, production and grazing management efficiency was demonstrated.