Slot coating is largely used in the manufacturing of different functional films, including battery electrodes. For optimum performance, the thickness of the film deposited over the moving substrate must be uniform along the cross-web direction. The flow uniformity is achieved by properly designing the geometry of the internal cavities of the coating die. The optimized design is strongly influenced by the liquid rheology, which needs to be accurately described in the flow models. The rheological behavior of particle suspensions, as those encountered in slot coating of battery electrodes, is very complex. The viscosity varies orders of magnitude with the shear rate, and they show thixotropic behavior. Usually, flow models used in the design of slot die cavities do not take into account the time dependency of particle suspensions and the flow is described assuming that the local viscosity is only a function of the local deformation rate. This can lead to inaccurate description of the flow, since the liquid structure does not change instantaneously after a step change to a new stress level. This study addresses the three-dimensional internal flow of thixotropic fluids. Time-dependent behavior is modeled using a kinetic equation for the material fluidity, which is defined as the reciprocal of viscosity, and specifies uniquely the material microscopic state. The model accounts for the mechanisms of buildup and breakdown of the microstructure with no postulated functions nor additional auxiliary parameters. A 3D finite element numerical model, implemented in Python, based on the precompiled library named Dolfin, developed within the open-source project FeniCs, allows for a realistic representation of thixotropic fluid flow in complex geometries, such as those present in the internal cavities of slot coating dies. The results show the effect of thixotropy in the flow behavior and how they should be included in the design of slot dies used for coating particle suspensions.