In recent decades, numerical calculations have often been used to optimise, from a technical and economical perspective, the design of underground works. Using these tools allows efficient and affordable designs to be obtained. Simulation of the tunnelling procedure when using a tunnel-boring machine and in urban areas is a complex soil–structure interaction problem. Here, a three-dimensional (3D) code using finite differences is used. The reference case of this study is Lyon metro line D project in France, where a non-symmetric load is present at the surface due to the presence of a retaining wall. An accurate on-site monitoring system was set up to assess ground movements during the mechanised excavation of twin tunnels. The collected data are used as a reference to show the validity and accuracy of the developed 3D model. Two constitutive models were used to simulate the soil behaviour: plastic hardening (PH) and linear elasticity with perfect plasticity (Mohr–Coulomb shear failure criterion). The Mohr–Coulomb constitutive model shows some drawbacks, which can be eliminated by using PH. The existence of a retaining wall induces a non-symmetric load condition; however, the settlement trough predicted by advanced numerical models shows good agreement with that obtained by monitoring data.