This dataset presents a time series of benthic invertebrate bycatch records collected during pelagic longline fishing operations targeting Patagonian toothfish (Dissostichus eleginoides) in the Prince Edward Islands region of the sub-Antarctic Southern Ocean from 2009 to 2023. The data were obtained from independent scientific observers aboard commercial vessels in accordance with Commission for the Conservation of Antarctic Marine Living Resources (CCAMLR) Conservation Measure 22-06, which mandates the reporting of taxa associated with Vulnerable Marine Ecosystems (VMEs). Each record includes an entry number, observer segment unique identifier, vessel unique identifier, observer logbook number, year the record was collected, line segment number, taxonomic code as given in 2009 CCAMLR VME guide, associated taxonomic name, bycatch weight at random segments per fishing line/set, gear type used, number of fishing hooks used at the specific segment, and anonymous vessel number. The dataset comprises 1,817 records spanning 32 benthic morphotypes. The raw dataset has not been validated and therefore dubious records exist. Nonetheless, Filander et al (2025) curated it for reusability and it's intended to support ecosystem-based fisheries management as reflected in CCAMLR Conservation Measure 22-06 and 22-07 notwithstanding the exemptions given to the area by CCAMLR, trait-based vulnerability assessments, and refinement of benthic threshold detection protocols under CCAMLR frameworks.