Conditions of low oxygen, as well as strong fluctuations in dissolved oxygen concentrations, can substantially affect marine benthic communities. An early assessment of the status of a community after such an event is of fundamental ecological importance and may help to inform management measures. This paper investigates the response of a foraminiferal assemblage, and its relationship with sediment bio-geochemistry, micro-organisms and other fauna, following experimentally induced hypoxia on an intertidal flat in the Scheldt Estuary, The Netherlands. Sediment hypoxia was induced during one experiment in winter and a second in late spring. The foraminiferal assemblages in the upper 0–1 cm of sediment were sampled at two and five months post-hypoxia. Changes in foraminiferal abundance and biovolume were compared to responses of microphytobenthos, bacteria, meiofauna and macrofauna, which have been reported in separate papers. The foraminiferal assemblage comprised three species, Haynesina germanica, Ammonia beccarii and Elphidium excavatum. Their species-specific abundance and estimated biovolume varied with timing of disturbance (winter vs. spring hypoxia) and the duration of recovery (2 vs. 5 months). Although all foraminiferal species were expected to benefit from recolonization of macrofauna, H. germanica was negatively correlated to the abundance of macrofaunal bioturbators during recovery. The abundance of A. beccarii was positively correlated with microalgal biomass. These findings revealed species-specific responses by foraminifera after hypoxia and the concomitant recovery of other biota, further demonstrating the usefulness of foraminifera as ecological indicators.