Hypoxia is one of the most important stressors affecting the health conditions of coastal ecosystems. In highly productive ecosystems such as the Humboldt Current ecosystem, the oxygen minimum zone is an important abiotic factor modulating the structure of benthic communities over the continental shelf. Herein, we study soft-bottom macrobenthic communities along a depth gradient–at 10, 20, 30 and 50 m–for two years to understand how hypoxia affects the structure of shallow communities at two sites in Mejillones Bay (23°S) in northern Chile. We test the hypothesis that, during months with shallow hypoxic zones, community structure will be much more dissimilar, thereby depicting a clear structural gradient with depth and correlated abiotic variables (e.g. organic matter, temperature and salinity). Likewise, during conditions of deeper hypoxic zones, communities will be similar among habitats as they could develop structure via succession in conditions with less stress. Throughout the sampling period (October 2015 to October 2017), the water column was hypoxic (from 2 to 0.5ml/l O2) most of the time, reaching shallow depths of 20 to 10 m. Only one episode of oxygenation was detected in June 2016, where normoxia (>2ml/l O2) reached down to 50 m. The structure of the communities depicted a clear pattern of increasing dissimilarity from shallow normoxic and deep hypoxic habitat. This pattern was persistent throughout time despite the occurrence of an oxygenation episode. Contrasting species abundance and biomass distribution explained the gradient in structure, arguably reflecting variable levels of hypoxia adaptation, i.e. few polychaetes such as Magelona physilia and Paraprionospio pinnata were only located in low oxygen habitats. The multivariable dispersion of community composition as a proxy of beta diversity decreased significantly with depth, suggesting loss of community structure and variability when transitioning from normoxic to hypoxic conditions. Our results show the presence of semi-permanent shallow hypoxia at Mejillones Bay, constraining diverse and more variable communities at a very shallow depth (10–20 m). These results must be considered in the context of the current decline of dissolved oxygen in most oceans and coastal regions and their impact on seabed biota.