Multiple measures of plant diversity are vital to understand the response of plant communities to changing environmental conditions in peatlands. We assessed whether functional, phylogenetic and taxonomic diversities of woody and herbaceous fen peatlands in East Anglia, UK varied between plant communities under different management practices (mowing and grazing). We adjusted the weight of phylogenetic distances in a combined functional-phylogenetic distance matrix to assess functional and phylogenetic diversities separately and in combination. We tested the phylogenetic signal of four traits (leaf dry-matter content, leaf N, leaf δ13C and leaf δ15N) and employed null models to determine patterns of clustering and over-dispersion of traits and phylogenies. We used rarefaction to determine if observed taxonomic diversity was higher or lower than expected. Functional, phylogenetic and taxonomic diversities varied across and within vegetation types. Annual grazing was associated with reduced functional and phylogenetic diversities but was not significantly associated with taxonomic diversity. Annual mowing was associated with increased phylogenetic and taxonomic diversities. Multiple diversity metrics can provide complementary or contrasting information. While there are benefits to annual management of wetlands (benefitting rare species), these must be weighed against eroding functional and phylogenetic diversities that can potentially adversely affect responses to environmental change. Communities mown every seven to eight years supported characteristic fen vegetation and maintained high plant diversity across a range of measures. Our results sound a cautionary note of neglecting to monitor multiple plant diversity measures in managed habitats, since attempts to maximize one may inadvertently lead to the erosion of others.