A sedimentary box core (BIAC072014) collected in a coastal environment in the Humboldt Current Ecosystem (HCE, Inglesa Bay, ~ 27°S, northern Chile) was used to reconstruct the changes in biological productivity and ocean-climate fluctuations during the last ~ 1.5 kyr via geochemical, mineralogical and micropaleontological analyses. From ~ 510 CE to ~ 930 CE, “El Niño-like” conditions prevailed, while during the Medieval Climate Anomaly (MCA, ~ 950 CE to ~ 1450 CE), “La Niña-like” conditions predominated. This pattern might have resulted from weakening/strengthening of the Walker cell, contraction/expansion of the South Pacific Sub-tropical High (SPSH) and a predominance of warm/cold phases of the Pacific Decadal Oscillation (PDO). Between ~ 1820 CE and the present, Inglesa Bay experienced a reduction in the Oxygen Minimum Zone (OMZ) intensity and biological productivity, an increase in the detritic input and a decrease in sea surface temperature (SST). Despite the regional intensification and secular cooling (~ 14°S and ~ 27°S) of coastal upwelling, the similarity between the reduction in biological productivity and OMZ intensity in this region and that in the central zone of Chile (~ 36°S) suggests that Inglesa Bay acts a transition zone in relation to the oceanographic behaviour of the HCE. The reduction in the OMZ intensity and biological productivity during the last ~ 200 years could be explained by greater subsurface ventilation in intermediate depths due to more northward displacement of the subduction region of the Eastern South Pacific Intermediate Water (ESPIW) near ~ 30°S in response to the strengthening of the circulation of the Subtropical Gyre. The coastal cooling observed in the northern section of HCE during the current Warm Period suggests that it is not possible to demonstrate that El Niño-like conditions promoted the reduction in biological productivity and OMZ intensity in Inglesa Bay.