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Temporal changes in host-associated microbiomes during host-dispersal processes are almost entirely unexplored, especially for hosts which undergo rare or stochastic dispersal. What little we do know has been gleaned from simulations or examination of microbiomes of hosts undertaking regular migratory movements, which might differ from less regular dispersal events. Here we directly examine the microbiomes of oceanic rafting seaweed, leveraging host genomic analyses, amplicon sequencing, and oceanographic modelling to study the impacts of stochastic ecological dispersal of hosts on the microbiome. We find that during their voyage, rafts tend to shift from a community dominated by core microbes to a community dominated by a few abundant taxa, and many rare taxa. Raft microbiomes rapidly diverge from those of non-rafts, with changes in selective pressures leading to major community changes and increased dysbiosis over the course of oceanic rafting. These data have particular significance under scenarios of increasing environmental variability such as those arising from climate change, where host range shifts are likely to lead to increased movement of hosts along broader ecological ranges.