Biodiversity can be measured at multiple organizational scales. While traditional studies have focused at taxonomic diversity, recent studies have emphasized the ecological importance of diversity within populations. However, it is unclear how these different scales of diversity interact to determine the consequence of species loss. Here we asked how predator diversity and presence of ontogenetic diversity within predator populations influences community structure. Ontogenetic diversity arises from shifts in the traits and ecology of individuals during ontogeny and it is one of the biggest sources of intraspecific diversity. However, whether it dampens or strengthens the negative consequences of with species loss is poorly understood. To study the interaction of species diversity and ontogenetic diversity, we experimentally manipulated predator species diversity and diversity of developmental stages within focal predator species and analysed their joint effect on predator and prey survival, biomass and prey community structure in experimental pond systems. While individual effects of ontogenetic diversity were often species specific, losing predator species from the community often had a much smaller or no effect on prey survival, biomass or community structure when all predator populations had high ontogenetic diversity. Thus, ontogenetic diversity within populations buffered against some of the consequences of biodiversity loss at higher organizational levels. Because the experiment controlled mean per capita size and biomass across structured versus unstructured populations, this pattern was not driven by differences in biomass of predators. Instead, results suggest that effects were driven by changes in the functional roles and indirect interactions across and within species. This indicates that even if all environmental conditions are similar, differences in the intrinsic structure of populations can modify the consequences of biodiversity loss. Together, these results revealed the importance of ontogenetic diversity within species for strengthening the resilience of natural communities to consequences of biodiversity loss and emphasize the need to integrate biodiversity patterns across organizational scales.