Abstract 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. To study the impact of a temperature increase on the geochemistry of some candidate clay host rocks considered in Europe, 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 (WRBC) and whole rock Opalinus Clay (WROPA) samples in contact with some representative pore waters at 90°C, the maximum temperature expected as a result of heat-emitting waste. The same experimental settings were applied to run parallel tests on the separated clay fractions (CFBC and CFOPA). The aim was to assess the impact of coupled heat and chemical processes on their mineral stability in the presence and absence of the organic matter and carbonates. At specific time intervals, the solids were separated from solutions and 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. In line with the experimental observations, the geochemical modelling suggests that minerals are able to reequilibrate relatively fast with the ambient solutions. The clay mineralogy was modified only in the case of Boom Clay deprived of carbonates and organic matter. The clay mineralogical alterations are associated with the increase of the layer charge, TSA and CEC. The experimental and modelling results indicate that coupled heat and perturbed geochemical conditions did not jeopardise the stability of the constituent minerals in the studied clays. Altogether, the presented work highlights very good buffer capacity of both candidate host rocks towards geochemical perturbations.