Merigliano et al. identified a non-canonical, “off-pore” role for nucleoporins in genome stability and in the spatial regulation of homologous recombination in multicellular eukaryotes. Nup98 condensates form at DNA breaks within pericentromeric heterochromatin to prevent aberrant recombination by excluding Rad51, while promoting the mobilization of repair sites through immiscibility with heterochromatin protein 1 (HP1) condensates.