A temperature increase coupled with other geochemical perturbations is expected to occur during the heat phase of the geological repository due to the presence of heat-emitting radioactive waste and engineered barrier system. We tried to simulate such conditions by means of batch tests followed by detailed mineralogy analysis and geochemical modelling. The batch tests were performed on whole rock Boom Clay and Opalinus Clay samples in contact with some representative pore waters at 90°C. The same experimental conditions were applied to separated clay fractions free from carbonates and organic matter. At specific time intervals, the solids were subject to (Q)XRD, FTIR, UV-VIS, TSA and CEC determinations. The whole rock samples were found stable irrespectively of the solution composition with no negative impact on their physico-chemical properties. The geochemical modelling suggests that minerals are able to reequilibrate relatively fast with the ambient solutions. The clay mineralogy was solely modified in the separated clay fraction of Boom Clay. The clay mineralogical alterations are associated with the increase of the layer charge, TSA and CEC. The results indicate that coupled heat and perturbed geochemical conditions have very limited impact on the mineral stability of the studied clays reflecting their good buffer capacity.