During early development, primordial germ cells (PGCs) migrate to the genital ridge, where they give rise to germ cells in the developing gonads. However, little is known about PGC activity after reaching their destination, at which point PGCs were presumed to be in a state of quiescence. However, René Ketting and colleagues now reveal that zebrafish PGCs undergo surprisingly dynamic changes shortly after their migration. Using microscopy and sequencing techniques, the authors provide detailed analyses of nucleus shape, RNA expression and chromatin structure in PGCs during early stages of gonad development. They reveal that 2 days after PGCs arrive at the genital ridge, their nuclei become strongly gyrated, causing cytoplasmic proteins to appear nuclear. Concurrently, there are changes to nuage (perinuclear space) density and compaction, potentially driven by the piRNA pathway, which also becomes activated in the cytoplasm at this stage. RNA polymerase 2 activity increases in post-migratory PGCs with a high level of transcription, including non-genic transcription from large loci. Importantly, many germ cell-specifying genes are only strongly expressed several days after migration, indicating that PGC commitment occurs relatively late in development. Overall, these data provide a detailed resource for a previously overlooked, but important, period in PGC development.