A key concept in theoretical ecology is the positive correlation between biodiversity and ecosystem stability. To test the relationship between diversity and community stability in host-associated microbiomes, we exposed six marine sponge species (Amphimedon queenslandica, Ianthella basta, Stylissa flabelliformis, Coscinoderma mathewsi, Cymbastela concentrica and Ircinia ramosa) with varying levels of microbial diversity to a non-lethal salinity change and followed their microbial composition over time using 16S rRNA gene amplicon sequencing. No visible signs of sponge stress were evident following salinity amendment and their microbiomes exhibited compositional resistance irrespective of their microbial diversity. However, microbiome composition varied significantly according to microbiome diversity (high versus low), between sponge species and even between conspecific sponge genotypes.