Identifying drivers that shape biodiversity across biogeographical regions is important to predict ecosystem responses to environmental changes. While β‐diversity has been widely used to describe biodiversity patterns across space, the dynamic assembly of species over time has been comparatively overlooked. Insights from terrestrial and marine studies on temporal β‐diversity has mostly considered environmental drivers, while the role of biotic mechanisms has been largely ignored. Here, we investigated patterns of temporal variation in β‐diversity of seagrass‐associated amphipods. We conducted a study in three biogeographical regions across a temperate to subtropical latitudinal gradient (approximately 2000 km, 13° of latitude in total). In each region, we randomly selected three Cymodocea nodosa meadows, totaling nine meadows sampled seasonally (i.e., four times per year) from 2016 to 2018. We partitioned temporal β‐diversity into its turnover (i.e., species replacement) and nestedness (i.e., differences in species composition caused by species losses) components and addressed the relative influence of both temporal variation in habitat structure (i.e., biotic driver) and environmental conditions on the observed β‐diversity patterns. Our study revealed high temporal β‐diversity of amphipod assemblages across the three biogeographical regions, denoting significant fluctuations in species composition over time. We identified species turnover as the primary driver of temporal β‐diversity, strongly linked to temporal variability in local habitat structure rather than to regional climatic drivers. Subtropical Atlantic meadows with high structural stability over time exhibited the largest turnover rates compared with temperate Mediterranean meadows, under lower structural stability, where nestedness was a more relevant component of temporal β‐diversity. Our results highlight the crucial role of habitat stability in modulating temporal β‐diversity patterns on animals associated with seagrasses, stressing the importance of monitoring variations in habitat structure over time for developing management plans and restoration actions in the context of diversity loss and fragmentation of ecosystems.