Alpha (α), beta (𝛽), gamma (𝛾) and zeta (𝛇) diversity metrics are complementary in their information, yet insight from this complementarity has yet to be explored. Here we use postglacial lake sediments for reconstructing plant metacommunity diversity patterns using all four metrics. Based on sedimentary ancient DNA data, we find that the metacommunity both diversified (𝛽_spatial) and homogenised (𝛇) over millennia of ecosystem development, alongside rising taxon richness at both community (α) and metacommunity (𝛾) level. In contrast temporal turnover of taxa (𝛽_temporal) declined, both at the community and metacommunity level. With taxon appearances exceeding disappearances this suggests the co-existence of taxa in the communities increased. However, the shared taxa in the metacommunity (𝛇) showed a continuously high temporal turnover, suggesting the taxa contributing to the metacommunity homogenisation were largely transient. That communities homogenised but remained distinctively different over millennia highlights the importance of individual communities in sustaining metacommunity biodiversity.