Grazing incidence X‐ray scattering during in‐situ annealing has been used to study the interface stability in MgO‐based electrodes and barriers in magnetic tunnel junctions (MTJs). In MTJs based on Co60Fe20B20/MgO, low temperature annealing at about 200 °C can result in a drop in the tunnelling magnetoresistance (TMR). Specular reflectivity measurements show a change in fringe structure at high scattering vector, at the temperature at which the TMR drops. Also, a change in diffuse scatter relative to the specular scatter is observed. Annealing of [Co60Fe60B20/MgO]×14 multilayers prepared by three different techniques shows no change in the specular Bragg peaks with no loss of Kiessig fringe structure on crystallization and no change in the diffuse scatter up to 200 °C. We suggest that diffusion of Mn from the IrMn pinning layer, present in the MTJs but not in the multilayers, may be responsible for the …