Nuclear transport is controlled by the nuclear pore complex (NPC) formed of nucleoporins (Nups). Although NPCs have been considered identical in function, recently, Nup expression has been shown to vary. Here, Mustafa Khokha and colleagues investigate the role of Nup107 – an NPC scaffold protein - during Xenopus development. They first show that Nup107 RNA and protein abruptly decrease following gastrulation. Loss-of-function experiments show an expansion of ectoderm in Nup107-deficient gastrula at the expense of mesoderm and endoderm. Using RNA sequencing of Nup107 knockdown embryos, the authors find an enrichment of transcripts normally degraded during the maternal-to-zygotic transition. Interestingly, these maternal transcripts are enriched for sites of the microRNA miR427, and they show that Nup107 knockdown reduces miR427 expression. miR427 overexpression rescues germ layer patterning of Nup107-depleted embryos. Furthermore, miR427 targets, such as rest, are elevated in Nup107-deficient embryos and are reduced by exogenous miR427 expression. To understand how Nup107 influences miR427 levels, the authors show that, in control embryos, pri-miR427 is abundant in the nucleus before gastrulation, but this localisation is lost upon Nup107 depletion. Together, these data suggest that Nup107-containing NPCs control pri-miR427 export during the maternal-to-zygotic transition and thus regulate maternal transcript degradation and gastrulation, providing context-specific roles for NPCs in development.