Changes in phenotypic variability in natural populations have received little attention in comparison with changes in mean trait values. This is unfortunate because trait diversity may influence adaptive evolutionary change and population stability. We combine two unique data sets to illuminate complex trait changes in Atlantic cod along the Norwegian Skagerrak coast: (i) an annual beach seine survey starting in 1919, monitoring juvenile body size and abundance and (ii) capture–mark–recapture data from which we estimated selection on juvenile body size and growth. We demonstrate that the variability of juvenile size has been steadily decreasing across nine decades, with no evidence for a similar trend in mean size. We also report that small, slow-growing fish as well as large, fast-growing fish are selected against. Together, these results suggest long-term stabilizing selection acting on Atlantic cod, and emphasize the need for further studies evaluating the full complexity of trait changes in wild populations.