Biodiversity is globally recognised as a cornerstone of healthy ecosystems, and biodiversity conservation is increasingly becoming one of the important aims of environmental management. Evaluating the trade-offs of alternative management strategies requires quantitative estimates of the costs and benefits of their outcomes, including the value of biodiversity lost or preserved. This paper takes a decision-analytic standpoint, and reviews and discusses the alternative aspects of biodiversity valuation by dividing them into three categories: socio-cultural, economic, and ecological indicator approaches. We discuss the interplay between these three perspectives and suggest integrating them into an ecosystem-based management (EBM) framework, which permits us to acknowledge ecological systems as a rich mixture of interactive elements along with their social and economic aspects. In this holistic framework, socio-cultural preferences can serve as a tool to identify the ecosystem services most relevant to society, whereas monetary valuation offers more globally comparative and understandable values. Biodiversity indicators provide clear quantitative measures and information about the role of biodiversity in the functioning and health of ecosystems. In the multi-objective EBM approach proposed in the paper, biodiversity indicators serve to define threshold values (i.e., the minimum level required to maintain a healthy environment). An appropriate set of decision-making criteria and the best method for conducting the decision analysis depend on the context and the management problem in question. Therefore, we propose a sequence of steps to follow when quantitatively evaluating environmental management against biodiversity.