The study of functional diversity has been gaining increasing prominence in Ecology, as a way of evaluating how the species traits affect ecosystem processes. Several empirical studies indicate a strong relationship between trait diversity and ecosystem attributes, and high values of functional diversity are an indication of the robustness of a given ecosystem. However, there are important theoretical differences between the studies that evaluated these relationships, which lead to relevant methodological differences. Here we will discuss the need to choose response and effect traits in a theoretically-sound manner, arguing for their choice based on their functional contribution to ecosystem process as conceived by the organizational theory of ecological functions. From this perspective, the contribution of effect traits to the organizational closure of an ecological system can provide a fundamental criterion for their choice in empirical studies. Similarly, we point out criteria for choosing response traits. Furthermore, we will argue that the new mechanistic philosophy of science can be used in studies of functional diversity as a way to robustly establish cause and effect relationships in empirical studies. Finally, we will model an example of the application of the approach proposed in the paper in pollination ecology, indicating its heuristic potential for empirical studies.