Abstract The Gulf of Corinth is a young (1 Ma) active rift currently extending N00, which displays significant contrasts in structural style along strike. A possible explanation for these variations is the presence of the Phyllades nappe in the basement of the western part of the Gulf. Previous 2D thermo-mechanical models have shown that a strong strength contrast between this metamorphic unit and the rest of the basement can explain the kinematics and the spacing of the faults in the western part. The rift, however, displays a wide variety of 3D features (e.g., en echelon faulting, N30 transverse normal faults) that cannot be taken into account using 2D modelling. To obtain 3D insights into the role of an inherited dipping weakness zone, analogue (sand and PDMS) experiments based on the results of the 2D numerical thermo-mechanical model have been performed. The analogue models show that a 30° discrepancy between the dipping direction of the weak nappe and the direction of extension leads to the formation of en echelon and N30 striking normal faults as observed in the Gulf of Corinth. However, fault spacing and graben width completely misfit both the data and the results of the thermo-mechanical models on which the analogue experiments were based. In order to understand those differences, numerical mechanical benchmarks of the analogue experiments have been run to test different factors (3D lateral displacements, values of the elastic parameters and bottom boundary conditions) that could have affected the dynamics of the analogue model. This approach highlights, for our case study, that the misfits are mostly related to the lack of isostatic compensation at the base of the analogue experiments.