The present special issue is devoted to the experimental, theoretical and computational studies of fundamental features in transport phenomena, structural and phase transitions in various soft and disordered systems (polymers, colloids, glasses, amorphous, crystalline, and composite materials) involved in macroscopically non-equilibrium processes (hydrodynamic flows; non-stationary deformations, heat and mass transfer and so on). Special attention is focused on a detailed microscopical study of the effects of internal structural and phase transformations on macroscopic physical properties and phenomena in the systems under study.