The reliability of solid oxide fuel cell (SOFC) systems is nowadays close to meet the requirements for market implementation. However, mechanical failures remain salient issues, which often limit the practical lifetime of SOFC stacks and directly impact the costs. To our knowledge, the capability for in-operando monitoring of the risks of their occurrence has not yet been demonstrated. Mechanical issues are typically identified indirectly once a critical failure already occurred, e.g. from cell open-voltage measurements. Therefore, numerical thermo-mechanical investigations are of high interest to understand and predict potential failure modes in SOFC stacks. Finite-element (FE) stack models commonly consider idealized components, i.e. computational domains imported from computer-aided design. In reality, the dimensions and geometry of the produced stack components have statistical variations, because of the imperfections of manufacturing processes and of the costs associated with component quality. In this study, production data shows that the interconnect is a component that is subject to such manufacturing tolerances. The resulting variability in shape, e.g. flatness and/or thickness, is expected to have an impact on the distribution of the contact pressure over the active area. Therefore, a dedicated measurement and simulation workflow has been developed to simulate the effects of component initial deformation. One repeating unit of an SOFC stack is meshed and implemented in the thermo-mechanical model here presented, to maintain the computational time at a few days on a workstation. Modified periodic boundary conditions are imposed on the upper and lower parts of the meshed domain to model the conditions at the middle of a large stack. The mechanical interaction between the components is modelled by softened contact or constrained node displacement, depending upon the interface. Further adjustments of the interface properties are performed during the analysis to account in a simplified manner for the stack conditioning steps, such as sintering of the contact pastes and crystallisation of the glass sealant. The material constitutive laws implemented in the model include (i) rate-independent elasto-plasticity and (ii) combined primary-secondary creep for the interconnect alloy and the anode cermet. Only secondary creep is considered for the materials of the other SRU parts. The elastic properties of the gas-diffusion layer (GDL) materials are estimated by computational homogenization. This allows the modelling of the GDLs as simplified continuum geometries to reduce the stack simulation runtime. The workflow for thermo-mechanical analysis developed in this study starts with the measurement of the deformation profile of several real interconnects, followed by implementation in the stack model, before the simulation of the stack assembly. Then, the stack conditioning procedure is simulated to account for the effects of the stack manufacturing on the stress-state just before operation. After this initialization step, the simulation of stack operation consists in importing temperature profiles from thermo-electrochemical simulations into the FE thermo-mechanical model. The simulated scenarios are either thermal cycling without operation or long-term operation in co-flow configuration at nominal conditions (0.4 A cm-2), interrupted by thermal cycles. For the considered design and for a given amplitude of initial interconnect deformations, the simulation results show that the distribution of the contact pressure over the active area can be already altered at the end of the stack qualification. In such cases, the GDLs cannot fully accommodate for the interconnect initial deformation, resulting in zones subjected to either higher or lower contact pressure, compared to the case of idealized initial components. This may lead to hot spots and locally pronounced irreversible deformations of the GDLs, among others, with potentially severe loss of contact pressure upon thermal-cycling or long-term operation. The stress in the sealant after thermal cycling increases after prolonged operation. In this situation, the regions of the sealants exposed to higher temperatures during long-term operation are subjected to larger stress at room temperature.