Microsites where seeds arrive during the dispersal process determine plant reproductive success, affecting the quality of dispersal. Despite their crucial role for plant recruitment, very few studies have addressed spatio-temporal variations in microsites of seed arrival in complex seed-disperser networks. Using an endozoochorous dispersal system, we characterized the microsites of seed arrival of eight fleshy-fruited plant species dispersed by five mammal species during two consecutive seasons across three sites in a Mediterranean environment (n = 383 feces with seeds; 261,453 seeds). We evaluated spatial and temporal variations in the probability of a seed to arrive at open microsites or at microsites with varying plant cover, considering selection by frugivores and assessing the extent to which seeds of particular species arrived under conspecifics or heterospecifics. We found strong spatio-temporal variations in the amounts of seeds of the eight target species arriving at different microsites. These variations were strongly driven by frugivores’ selection of different landscape elements (i.e. open areas and microsites dominated by different plant species), which differed from expectations based on their local availability. In general, more seeds than expected arrived at vacant (open) microsites. Using bipartite network graphs to connect seeds with their arrival microsites, we found that the proportion of seeds of fleshy-fruited species arriving near conspecifics or heterospecifics, or at vacant microsites, varied depending on the target plant species, but also on the frugivore species dispersing it, on the study site and on the dispersal season. Our study revealed marked spatio-temporal variations in the microsites of seed arrival, which will potentially have implications for the quality of dispersal effectiveness, ultimately affecting plant population dynamics and community structure. Such a strong context-dependence in the microsites of seed arrival is likely to confer resilience against unpredictable environmental conditions, like those typical of Mediterranean ecosystems.