The relative importance of local, regional and historical factors in controlling the spatial patterns of plant species distribution is still poorly known and challenging for conservation ecology. We conducted an empirical study to link the spatial variation of species and environments among forest patches embedded in contrasted agricultural matrices. We compared how forest herb communities responded to spatial environmental gradients and past forest cover. We found low values of β-diversity in both unfragmented and highly fragmented systems, independently from local and regional diversities. As fragmentation increased, the spatial structure of local plant communities was more complex and spatial effects explained an increasing proportion of β-diversity, suggesting that the importance of dispersal limitations increased and played out at broad spatial scales. However, where spatio-temporal isolation of forest patches was the highest, local species assemblages could not be explained, suggesting that the metacommunity functioning was disrupted. Where the historical continuity was high, local environmental characteristics explained a significant amount of species assemblages within metacommunities, suggesting habitat-selection processes. Beta-diversity and variations in presence–absence of species were also influenced by the intensity of landscape management, via the permeability of both forest edges and the matrix. This spatially-explicit analysis of metacommunities revealed that forest fragmentation impacts beta-diversity by altering not only the relative importance of deterministic and stochastic processes, but also the spatial scales at which they act. These results provide empirical support for the conservation of ancient forests and the maintenance of a high connectedness between fragments within agricultural landscapes.