Over the past two decades, El Nino events have weakened on average and their sea surface temperature (SST) anomalies shifted westward towards the central Pacific. Moreover, the intertropical convergence zone (ITCZ), which typically migrates southward from its northerly position during El Nino events, has not crossed the Equator since 1998. The causes of these changes remain under debate1–5. Here, using in situ, satellite and atmospheric reanalysis data, we show they can be related to a multidecadal strengthening of cross-equatorial winds in the eastern Pacific. This gradual strengthening of meridional winds is unlikely to be caused by El Nino/Southern Oscillation (ENSO) changes, and contains signals forced both locally and from outside the tropical Pacific, probably from the tropical North Atlantic. Coupled model simulations in which the observed cross-equatorial wind strengthening is superimposed successfully reproduce the key features of the recent changes in tropical climate. In particular, the tropical mean state experiences a ‘La Nina-like’ change, the ENSO amplitude weakens by about 20%, the centre of the SST anomalies shifts westward and the ITCZ now rarely crosses the Equator. Thus, cross-equatorial winds are found to modulate tropical Pacific mean state and variability, with implications for quantifying projected changes in ENSO under anthropogenic warming. In recent years, El Nino sea surface temperature anomalies have weakened and shifted westward. Observational and model analyses reveal these changes can be related to a multidecadal strengthening of cross-equatorial winds, forced both locally and from the tropical Atlantic.