A bench-scale self-forming dynamic membrane bioreactor (SFD MBR) treating canning wastewater showed instable filtration performance, with a worsening in correspondence of a change in the influent quality. To unveil the possible reasons for such behaviour, a microbial investigation was carried out to complement conventional filterability and settleability tests. The microbial communities of the influent wastewater, the activated sludge, and the filtering sludge cake (dynamic membrane) were characterised through metagenomic and differential abundance analyses. In parallel, the production of exopolymers was measured. The outputs indicate that under the tested conditions the canning wastewater promoted the development of a very peculiar microbial ecosystem, with a strong selection of the genus Thiothrix (relative abundance above 90 %). The Shannon index values in activated sludge were below 2, indicating a very low bacterial diversity. This may have limited the ecosystem resilience towards changes of external conditions, causing instability in the process of the dynamic membrane formation. Furthermore, the diversity analysis showed that the bacterial compositions of the feed and the sludge resulted not significantly linked to each other, confirming the main role of the chemical composition of the influent wastewater on overall process performances. When treating agro-industrial streams, in-depth feed characterisation is recommended in order to prevent the factors that may generate instability in SFD MBR performance.