The 3D organization of the genome has emerged as an important regulator of cellular development. Post-mitotic neurons undergo conserved changes in genome organization, such as the inward radial repositioning of heterochromatin-rich chromosomes as they differentiate. Additionally, transcriptionally active but heterochromatin-associated gene-dense (hGD) regions significantly strengthen their long-distance interactions during cerebellar development. However, the specific developmental stages during which these nuclear changes take place have remained poorly defined. Here, we report that hGD regions relocalize toward the nuclear interior and strengthen their chromosomal interactions as immature granule neurons transition from active cell migration to subsequent stages of neuronal differentiation. During this period, hGD genomic regions are coordinately repositioned in the nucleus alongside their physically tethered heterochromatic chromocenters. Despite these major changes in nuclear organization, the hGD subcompartment remains distinct from other transcriptionally active or repressive nuclear bodies, including heterochromatic chromocenters, throughout development. Notably, these nuclear changes appear to be independent of transcriptional changes that occur during granule neuron differentiation. Together, our results provide insights into the developmental timing of structural changes in the chromosomes of post-mitotic neurons.