Helium bubbles are known to form in nuclear reactor structural components when displacement damage occurs in conjunction with helium exposure and/or transmutation. If left unchecked, bubble production can cause swelling, blistering, and embrittlement, all of which substantially degrade materials and—moreover—diminish mechanical properties. On the mission to produce more robust materials, nanocrystalline (NC) metals show great potential and are postulated to exhibit superior radiation resistance due to their high defect and particle sink densities; however, much is still unknown about the mechanisms of defect evolution in these systems under extreme conditions. Here, the performances of NC nickel (Ni) and iron (Fe) are investigated under helium bombardment via transmission electron microscopy (TEM). Bubble density statistics are measured as a function of grain size in specimens implanted under similar conditions. While the overall trends revealed an increase in bubble density up to saturation in both samples, bubble density in Fe was over 300% greater than in Ni. To interrogate the kinetics of helium diffusion and trapping, a rate theory model is developed that substantiates that helium is more readily captured within grains in helium-vacancy complexes in NC Fe, whereas helium is more prone to traversing the grain matrices and migrating to GBs in NC Ni. Our results suggest that (1) grain boundaries can affect bubble swelling in grain matrices significantly and can have a dominant effect over crystal structure, and (2) an NC-Ni-based material can yield superior resistance to irradiation-induced bubble growth compared to an NC-Fe-based material and exhibits high potential for use in extreme environments where swelling due to He bubble formation is of significant concern.