In recent years, scientific methods of bio- and geoarchaeology have become increasingly important for archaeological research. Political changes since the 1990s have reshaped the archaeological community. At the same time environmental topics have gained importance in modern society, but the debate lacks an historical understanding. Regarding medieval rural archaeology, we need to ask how this influences our archaeological research on medieval settlements, and how ecological approaches fit into the self-concept of medieval archaeology as a primarily historical discipline. Based mainly on a background in German medieval archaeology, this article calls attention to more complex ecological research questions. Medieval village formation and the late medieval crisis are taken as examples to sketch some hypotheses and research questions. The perspective of a village ecosystem helps bring together economic aspects, human ecology and environmental history. There are several implications for archaeological theory as well as for archaeological practice. Traditional approaches from landscape archaeology are insufficient to understand the changes within village ecosystems. We need to consider social aspects and subjective recognition of the environment by past humans as a crucial part of human–nature interaction. Use of the perspective of village ecosystems as a theoretical background offers a way to examine individual historical case studies with close attention to human agency. Thinking in terms of human ecology and environmental history raises awareness of some interrelations that are crucial to understanding past societies and cultural change.