1. Previous evidence suggests that bacterially mediated decomposition of complex organic substrates increases with greater food web diversity. We attempted to identify changes in bacterial community composition and function associated with increased decomposition in more diverse food webs. 2. We used aquatic microcosms where we manipulated productivity with different initial nutrient concentrations. We created a diversity gradient by establishing communities of eukaryotes with zero (bacteria alone), one, two or four microbe species (protists and rotifers) in each of four trophic levels: producers, herbivores, bacterivores and predators. The initial bacterial community was standardized across all treatments. To determine effects of productivity and diversity on the bacterial community, we measured: decomposition, abundance, diversity of colony morphotypes (a measure of composition) and community level physiological profiles (CLPP) (a functional profile based on carbon substrate utilization). 3. Decomposition increased with greater eukaryotic species richness and was not influenced by productivity. Bacterial abundance remained constant with increasing eukaryotic species richness at low productivity, but significantly declined at high productivity. Eukaryotic species richness together with productivity influenced the composition of the bacterial community. However, the CLPP was strongly influenced by productivity and not species richness. 4. Food web diversity and productivity interact to influence bacterial community composition and function. In more diverse food webs, bacterial activity (decomposition) increased despite lower population abundance.