Controlling magnetic order on ultrafast timescales, driven by spintronic and recording applications, is one of the main directions of current research in magnetism. Despite major advances in understanding the temporal evolution of magnetic order upon its emergence or quenching, experimental demonstration of the local link between microstructure and dynamic nucleation is missing. Here, taking advantage of the high structural and magnetic resolution of in situ transmission electron microscopy, we observe that cumulative laser irradiation significantly alters the nucleation pathway of the first-order antiferromagnetic to ferromagnetic phase transition of FeRh thin films, causing the transition to switch from homogeneous to heterogeneous nucleation. This leads to a decrease of 20 K in transition temperature and the emergence of submicron magnetic vortices as preferential nucleation motifs. These vortices are pinned in the film by underlying dislocation networks. We observe that the dislocation networks are formed and rearranged upon repeated crossing of the phase transition using both femtosecond and picosecond laser pulses. Our results establish a direct link between defect formation and the microscopic morphology of the nucleated ferromagnetic phase, with broad implications for ultrafast stroboscopic experiments and defect-mediated phase transitions in functional materials.