The formalization of ‘informal’ customary land rights is at the core of current rural land policies in Africa. The dubious impacts of such policies on agricultural production, and the recomposition of land rights and governance they cause, have been studied widely. But their territorial dimensions are hardly acknowledged. Studying the implementation of a rural land rights formalization project in central Benin, this article highlights the links between territorialization and plot-level land rights formalization. It first unpacks the notion of the village and presents a conceptual framework for analysing the superimposition of and contradiction between customary and administrative territories. Using two case studies, it then examines the conflicts that arise during formalization operations and their outcomes in terms of the mapping of land rights and political and administrative change. This article shows how the political organization of the territory and the socio-spatial inequalities resulting from the history of settlement shape the results of plot-level land rights registration (which explains why large parts of village territories have not been registered), and, in turn, how these registration operations lead to new territorialization processes and increase the heterogeneity of land tenure rights within the territory.