A robust computational method to study thixotropic multiphase fluids was developed using Smooth Dissipative Particle Dynamics (SDPD) [1], and accounting for surface tension effects as proposed by Tartakosky [2]. This methodology is able to consistently model both Newtonian and non-Newtonian fluids through the application of a thixotropic model to approximate the transient behavior of viscosity [3]. The model was rigorously validated through a series of static and dynamic benchmark tests to demonstrate the capability to handle the effects of interfacial tension between different phases. This includes the formation and dynamics of droplet suspensions, as well as the transport of single-phase and two-phase flows in channels. A number of exploratory cases were carried out in order to assess the developed model's capabilities. First, the approach was applied to investigate Liquid-Liquid Phase Separation process (LLPS), allowing to examine how variations in intrinsic parameters, such as surface tension and viscosity, influence its behavior. The applicability of the model was then extended to the study of channels with thixotropic multiphase flows in both continuous-continuous and continuous-disperse (droplet arrays) phase interactions. The results of the validation and exploratory cases show that the suggested methodology is capable of accurately capturing intricate multiphase phenomena and is applicable to a broad variety of relevant physical processes, varying from biological to industrial applications.