Abstract Accounting for the variation that occurs within species in food webs can theoretically result in significant changes in both network structure and dynamics. However, there has been little work exploring their role with empirical data. In particular, the variation associated with species’ life cycles, which is prevalent and represents both trait variation and taxonomic identity, has received little attention. Here, we characterize the structural consequences of life stage variation in five food webs, including a newly compiled web from the Arabian Gulf. We show that making life stage variation explicit in food webs results in larger food webs that possess consistent structural changes that are separate from the changes in structure that come simply from increasing the number of nodes in the webs. Furthermore, we show that the magnitude of these changes is related to ontogenetic specialism, the degree of overlap in the ecological niches of life stages. These results demonstrate the capacity of intraspecific variation to affect ecological networks and indicate the potential usefulness of stage‐structured food webs, which capture size and taxonomic information, to represent variation below the species level.