In situ small angle X-ray scattering (SAXS) was used to investigate the formation of higher-order morphologies in vinyl acetate (VAc) polymerization-induced self-assembly (PISA). Poly(ethylene glycol) (PEG) bearing a xanthate chain end was used as a hydrophilic macromolecular chain transfer agent in the macromolecular design via interchange of xanthates (MADIX)-mediated aqueous emulsion polymerization of VAc (see P. Galanopoulo, et al., Poly. Chem., 2020, 11, 3922–3930). In situ SAXS monitoring confirmed that the PISA process occurs in three steps: the nucleation of PEG₄₅-b-PVAc₂₀₀ block copolymer primary particles, a rapid morphological transition, and a final step in which the nano-objects grow slowly to their final dimensions. The transition step appears to be critical for the formation of higher-order morphologies through the aggregation of primary particles into larger clusters and their subsequent reorganization. Our results show that the transition step is extremely fast, making it highly sensitive to small perturbations. This explains why higher-order morphologies are usually obtained within a narrow window of conditions and often as a mixture. Furthermore, the morphological evolution observed in parallel static experiments appears to be more gradual than in in situ SAXS experiments, suggesting that in our system the sampled latexes were not thermodynamically stable and continued to evolve after sampling. Therefore, the sampling method may not provide a realistic view of the morphological transition during the reaction process in this system.