The vertical structure of temperature trends in the northeastern Atlantic (NEA) is investigated using a blend of Argo and hydrography data. The representativeness of sparse hydrography sampling in the basin mean is assessed using a numerical model. Between 2003 and 2013, the NEA underwent a strong surface cooling (0–450 m) and a significant warming at intermediate and deep levels (1000 m to 3000 m) that followed a strong cooling trend observed between 1988 and 2003. During 2003–2013, gyre‐specific changes are found in the upper 1000 m (warming and cooling of the subtropical and subpolar gyres, respectively), while the intermediate and deep warming primarily occurred in the subpolar gyre, with important contributions from isopycnal heave and water mass property changes. The full‐depth temperature change requires a local downward heat flux of 0.53 ± 0.06 W m−2 through the sea surface, and its vertical distribution highlights the likely important role of the NEA in the recent global warming hiatus.