We develop a general and unifying methodology for ecological economics which integrates philosophical considerations on the foundations of ecological economics with an adequate operationalization. We argue that the subject matter and aims of ecological economics require a specific combination of inter- and transdisciplinary research, and discuss the epistemological position on which this methodology is based. In accordance with this understanding of inter- and transdisciplinarity and the underlying epistemological position, we develop an operationalization which comprises simultaneous analysis on three levels of abstraction: concepts, (generic) models and case studies. This provides a systematic and integral view on ecological economics, and thus allows one to see the relationship between contributions to the field that have so far been perceived as very heterogeneous and largely unrelated. At the same time, this methodological framework may provide orientation for the further development of ecological economics.