The accumulation of non-heme iron in the brain has been proposed as a harbinger of neural and cognitive decline in aging and neurodegenerative disease, but support for this proposal has been drawn from cross-sectional studies, which do not provide valid estimates of change. Here, we present longitudinal evidence of subcortical iron accumulation in healthy human adults (age 19–77 at baseline). We used R2* relaxometry to estimate regional iron content twice within a 2 year period, measured volumes of the striatum and the hippocampus by manual segmentation, and assessed cognitive performance by working memory tasks. Two-year change and individual differences in the change of regional volumes, regional iron content, and working memory were examined by latent change score models while taking into account the age at baseline and metabolic risk indicators. Over the examined period, volume reduction occurred in the caudate nucleus and hippocampus, but iron content increased only in the striatum, where it explained shrinkage. Higher iron content in the caudate nucleus at baseline predicted lesser improvement in working memory after repeat testing. Although advanced age and elevated metabolic syndrome risk were associated with greater iron content in the putamen at baseline, neither age nor metabolic risk influenced change in any variable. Thus, longitudinal evidence supports the notion that accumulation of subcortical iron is a risk factor for neural and cognitive decline in normal aging.