Aging is a multifactorial biological process resulting in physiological and cellular decline. However, our understanding of age-related changes in 3D genome organization and the effect of external interventions on this process, remains limited. Here we performed low input Promoter Capture Hi-C (liCHi-C) and RNA-seq in hippocampal neurons of young and old mice which were also exposed to environmental enrichment (EE). In this study, we characterized the impact of age and cognitive and physical stimulation on chromatin interactome organization and gene expression. This dataset contains processed data and additional files related to the manuscript.