Food webs can respond in surprising and complex ways to temporary alterations in their species composition. When such a perturbation is reversed, food webs have been shown to either return to the pre-perturbation community state or remain in the food web configuration that established during the perturbation. Here we report findings from a replicated whole-lake experiment investigating food web responses to a perturbation and its consecutive reversal. We could identify three distinct community states in the food web that corresponded to the periods before, during and after the perturbation. Most importantly, we demonstrate the establishment of a distinct post-perturbation food web configuration that differed from both the pre- and during-perturbation communities in phytoplankton biomass and micro- and mesozooplankton species composition. We suggest that the pre- and post-perturbation food web configurations may represent two alternative stable community states. We provide explanations for how each of the contrasting communities may be maintained through altered species interactions. These findings add to the discussion of how natural food webs react to environmental change and imply that the range of potential ecosystem dynamics in response to perturbations can be wider and more complex than is often recognized.