Deoxygenation is a major threat to the coastal ocean health as it impacts marine life and key biogeochemical cycles. Understanding its drivers is crucial in the thriving and highly exploited Peru upwelling system, where naturally low-oxygenated subsurface waters form the so-called oxygen minimum zone (OMZ), and a slight vertical shift in its upper limit may have a huge impact. Here we investigate the long-term deoxygenation trends in the upper part of the nearshore OMZ off Peru over the period 1970–2008. We use a unique set of dissolved oxygen in situ observations and several high-resolution regional dynamical-biogeochemical coupled model simulations. Both observation and model present a nearshore deoxygenation above 150 m depth, with a maximum trend of – 10 µmol kg−1 decade1, and a shoaling of the oxycline depth (− 6.4 m decade−1). Model sensitivity analysis shows that the modeled oxycline depth presents a non-significant (+ 0.9 m decade−1) trend when remote forcing is suppressed, while a significant oxycline shoaling (− 3 m decade−1) is obtained when the wind variability is suppressed. This indicates that the nearshore deoxygenation can be attributed to the slowdown of the near-equatorial eastward currents, which transport oxygen-rich waters towards the Peruvian shores. The large uncertainties in the estimation of this ventilation flux and the consequences for more recent and future deoxygenation trends are discussed.