Equatorial deep jets (EDJs) are a prominent flow feature of the equatorial Atlantic below the Equatorial Undercurrent down to about 3000 m. Here we analyze long‐term moored velocity and oxygen observations, as well as shipboard hydrographic and current sections acquired along 23°W and covering the depth range of the oxygen minimum zones of the eastern tropical North and South Atlantic. The moored zonal velocity data show high‐baroclinic mode EDJ oscillations at a period of about 4.5 years. Equatorial oxygen observations which do not resolve or cover a full 4.5‐yr EDJ cycle nevertheless reveal large variability, with oxygen concentrations locally spanning a range of more than 60μmol kg−1. We study the effect of EDJs on the equatorial oxygen concentration by forcing an advection‐diffusion model with the velocity field of the gravest equatorial basin mode corresponding to the observed EDJ cycle. The advection‐diffusion model includes an oxygen source at the western boundary and oxygen consumption elsewhere. The model produces a 4.5‐yr cycle of the oxygen concentration and a temporal phase difference between oxygen concentration and eastward velocity that is less than quadrature, implying a net eastward oxygen flux. The comparison of available observations and basin‐mode simulations indicates that a substantial part of the observed oxygen variability at the equator can be explained by EDJ oscillations. The respective role of mean advection, EDJs, and other possible processes in shaping the mean oxygen distribution of the equatorial Atlantic at intermediate depth is discussed. Key Points Equatorial deep jets strongly affect oxygen distribution/variability Mean oxygen distribution in the equatorial Atlantic at intermediate depth Gravest equatorial basin mode forces an advection‐diffusion model