Abstract Structurally-complex habitats harbour more taxonomically-diverse and more productive communities, a phenomenon generally ascribed to habitat complexity relaxing the strength of interspecific predation and competition. Here, we challenge this classical, community-centred view by showing that positive habitat complexity-productivity relationships may also emerge from between-age-class, intra- specific interactions at a single-population level. In replicated outdoor pond populations of the medaka fish ( Oryzias latipes ), structurally complex habitats provide refuges to newborns and relax the strength of cannibalism, resulting in increased survival of age-0+ individuals, in a 80 % increase in population growth rate, and in dampened negative density-dependence indicating elevated habitat carrying capacity. The resultant higher population density in complex habitats was associated with increased competition for food among age-0+ and age-1+ individuals, as revealed by their smaller and more variable body sizes. Positive habitat complexity-productivity relationships may thus be considered as a generally-emergent property of both size-structured communities and populations, in which a larger body size brings a predation advantage. Our results highlight that anthropogenic habitat simplification drives biodiversity loss not only from community- but also from population-level processes, and hence may further reduce population productivity in the surviving species. Enhancement of habitat structural complexity is therefore a pivotal action for biodiversity improvement, not only in the context of ecosystem management, but also for successful conservation of endangered populations.