Understanding the flow instabilities encountered by the turbocharger compressor is an important step toward improving its overall design for performance and efficiency. While an experimental study using Particle Image Velocimetry was previously conducted to examine the flow field at the inlet of the turbocharger compressor, the present work complements that effort by analyzing the flow structures leading to stall instability within the same impeller. Experimentally validated three-dimensional computational fluid dynamics predictions are carried out at three discrete mass flow rates, including 77 g/s (stable, maximum flow condition), 57 g/s (near peak efficiency), and 30 g/s (with strong reverse flow from the impeller) at a fixed rotational speed of 80,000 rpm. Large stationary stall cells were observed deep within the impeller at 30 g/s, occupying a significant portion of the blade passage near the shroud between the suction surface of the main blades and the pressure surface of the splitter blades. These stall cells are mainly created when a substantial portion of the inlet core flow is unable to follow the impeller’s axial to radial bend against the adverse pressure gradient and becomes entrained by the reverse flow and the tip leakage flow, giving rise to a region of low-momentum fluid in its wake. This phenomenon was observed to a lesser extent at 57 g/s and was completely absent at 77 g/s. On the other hand, the inducer rotating stall was found to be most dominant at 57 g/s. The entrainment of the tip leakage flow by the core flow moving into the impeller, leading to the generation of an unstable, wavy shear layer at the inducer plane, was instrumental in the generation of rotating stall. The present analyses provide a detailed characterization of both stationary and rotating stall cells and demonstrate the physics behind their formation, as well as their effect on compressor efficiency. The study also characterizes the entropy generation within the impeller under different operating conditions. While at 77 g/s, the entropy generation is mostly concentrated near the shroud of the impeller with the core flow being almost isentropic, at 30 g/s, there is a significant increase in the area within the blade passage that shows elevated entropy production. The tip leakage flow, its interaction with the blades and the core forward flow, and the reverse flow within the impeller are found to be the major sources of irreversibilities.