Irregular urchins exclusively live in marine soft bottom habitats, dwelling either upon or inside sediments and selectively picking up sediment grains and organic particles, or swallowing bulk sediment to feed on the associated organic matter. The exact food source and dietary requirements of most irregular echinoids, however, remain incompletely understood. The schizasterid species Abatus cordatus (Verrill, 1876) is a sub-Antarctic spatangoid that is endemic to the Kerguelen. The feeding behaviour of A. cordatus was investigated using simultaneously metabarcoding and stable isotope approaches. Comparison of ingested and surrounding sediments by metabarcoding revealed a limited selective ingestion of prokaryotes and eukaryotes by the urchin. Compared to surrounding sediments, the gut content had (i) higher carbon and nitrogen concentrations potentially due to selective ingestion of organic matter and/or the sea urchin mucus secretion and (ii) δ15N enrichment due to the selective assimilation of lighter isotope in the gut. Feeding experiments were performed using 13C and 15 N-enriched sediments in aquariums. The progression of stable isotope enrichment in proximal and distal parts of the digestive track of A. cordatus revealed that all particles are not similarly transported likely due to siphon functioning. Ingestion of water with associated dissolved and particulate organic matter should play an important role in urchin nutrition. A. cordatus had a gut resident time fluctuating between 76 and 101 h and an ingestion rate of 36 mg dry sediment h−1 suggesting that dense populations of the species may play a key ecological role through bioturbation in soft bottom shallow-water habitats of the Kerguelen Islands.