Some of the most common liquid-like formulations rooted in the coating industry consist of rheologically complex structured materials such as inks, paints, and slurries. Yet, the impact of time-dependent structuring effects due to thixotropy on thin film coating applications remains elusive and still unclear. Here, we present a computational study of the effects of thixotropy on slot coating of time-dependent structured materials. By coupling a recent fluidity-based constitutive model for thixotropic materials with a well-established finite element/elliptic mesh generation method for free surface flows, we assess the role of thixotropy by comparing the predictions from the thixotropic model with those from a simple Generalized Newtonian Fluid model that uses the same flow curve for the material steady-state equilibrium viscosity. We find that thixotropy can indeed have a major impact on slot coating applications, potentially bringing strong implications not only to the flow dynamics but also to the operating limits of the process. In conclusion, the results and discussions we present in this study underscore the importance of accounting for thixotropy to genuinely model and fundamentally understand the behavior of time-dependent structured materials with complex rheology in processing flows like those ubiquitous across the broad fields of coating science and engineering.