Colonial ascidians are prolific and successful marine invertebrates worldwide. Colonial ascidians harbour a diverse assemblage of microorganisms, some of which are known to produce secondary metabolites (bioactives) that contribute to the ascidians’ ecological success. However, little is known about the microbial ecology of the putative symbionts associated with colonial ascidians and whether they consistently contribute to host competitiveness. We hypothesise that the colonial ascidian microbiome is host-specific and enables host ecological success in interacting with proximate competitor(s) through chemical competition facilitated by inducible microbially synthesised metabolites. We further theorise that, during invasion events, non-native colonial ascidians outcompete native ones using allelochemical capacities conferred by their microbiome and that nonnative colonial ascidians, which are globally successful invaders, harbour unique microorganism assemblages. To examine our hypotheses, it is necessary to characterise the relationship between ascidian ecological status (i.e., native, non-native, monospecific, or interacting) and the ascidian microbiome. We systematically sampled colonial ascidian specimens (both native and non-native species) engaged in competitive interactions as well as monospecific specimens. Microbiome analysis was conducted using 16S rRNA gene PCR amplicon sequencing to characterise baseline variability and identify microbial response patterns linked to the ecological status of host species. Our findings revealed a high degree of species-specificity in the ascidian microbiome, and native and non-native species exhibited distinct microbial patterns linked with their ecological state. However, interacting ascidian species did not appear to harbour dominant unique microbial assemblages compared to their monospecific counterparts. We also conducted the first microbiome comparison for zooids and tunics of colonial ascidians and found that, contrary to common assumptions, zooids and tunics generally harbour similar microorganisms. This study provides the first systematic characterisation of the colonial ascidian microbiome. We generated statistically informative baselines for the colonial ascidian microbiome and novel insight on its potential roles in mediating host ecology. Findings from this study form a robust foundation for future chemical characterisation of potential bioactive compounds (using the same specimens) and shotgun metagenomic analyses of these unique microbial communities.