The historical conditions under which bacterial lineages evolve determine their functional traits, and consequently their contribution to ecosystem functions (EFs). Under significant trait conservatism, which is common in prokaryotes, phylogeny may track the evolutionary history of species and predict their functionality. Productive communities can arise from: (i) the coexistence of functional, and therefore phylogenetically distant lineages, producing high EF rates at large phylogenetic diversity (PD); (ii) the dominance of productive lineages that outcompete other clades, generating high EF at low PD. Community composition will modulate the PD-EF relationship: The effects of anciently divergent lineages, whose deeply conserved functions determine the occupancy of major niches, may differ from that of recently divergent lineages showing adaptations to current conditions. We hypothesized that, in our model Mediterranean ecosystem, EF can be explained both by competitive superiority of ancient lineages and functional complementarity of recent lineages. To test this hypothesis, we sequenced a phylogenetic marker targeting bacteria across 28 soil plots and quantified EF related to microbial productivity, decomposition and nutrient cycling. Plots accumulating recently divergent lineages consistently showed higher EF levels that were slightly modified by the accumulation of ancient lineages. We discuss the assembly processes behind these phylogenetic-scale disparities and the final outcome in terms of ecosystem functioning.