The aim of sustainable heavy‐metal management in agroecosystems is to ensure that the soil continues to fulfill its functions: in agricultural production, in environmental processes such as the cycling of elements, and as a habitat of numerous organisms. To understand and manage heavy‐metal flows effectively, a consistent approach to modeling the flows is needed within the particular agro‐system under study. General aspects of heavy‐metal balance studies in agro‐ecosystems were described in part I of this study. In this article (part II), several European studies of heavy‐metal balances at varying spatial scales and in a variety of agro‐ecosystems are reviewed. Sectoral studies at the national and international levels provide information for economic analyses and generic regulations; however, policies implemented at these levels often ignore farm characteristics and individual management options. Field‐scale and farm‐gate balances give farmers specific feedback on effective options for better heavy‐metal management. Heavy‐metal balances could be incorporated in an environmental management system of certified farms. In this way, farm certification may well serve as a basis from which to develop policy to address environmental issues in agriculture.