The aim of this study was to disentangle the effects of landscape configuration (i.e., fragment area, connectivity, and proximity to a busy highway) on the assembly of annual plant communities at different spatial scales. Our main hypothesis was that larger and more connected fragments would have higher species densities per plot and this may result in differences in turnover and nestedness patterns at the fine spatial scales where plants interact. Specifically, since Mediterranean annuals are known to form strong competitive hierarchies, we expected to find a nested pattern of beta diversity due to sequential species loss. The study area was a fragmented gypsum habitat in central Spain with a semiarid climate where two fragmentation drivers coexist: agricultural practices and a roadway. Larger fragments had higher species densities per plot (20×20m). Nevertheless, we detected no effect on the species assembly at fine spatial scales (30×30cm). However, when the fragment connectivity was high the species that appeared in poor quadrats (30×30cm) comprised a subset of the species in rich quadrats. These results agree well with the establishment of strong competitive hierarchies among annual species. The distance to the highway influenced the identity of the species established in the community (i.e., species composition) at fine spatial scales, but we detected no effect on species turnover, nestedness, or species densities. The main conclusion of our study is that the effects of habitat fragmentation extend beyond the landscape scale and they determine the spatial assembly at fine spatial scales.