Autonomous underwater vehicles have seen widespread adoption across industrial, scientific, and defence applications. They are typically utilized to perform oceanic mapping, surveillance, and inspection-type missions. Hovering AUVs, used for inspection applications, are over-actuated vehicles incorporating multiple thrusters to enable multiple degrees of freedom control at a low velocity. These vehicles, however, are extremely energy-limited, owing to their restrictive structural design that prohibits large batteries. This necessitates careful hydrodynamic design to best utilize this limited energy storage. Of particular importance are the hydrodynamic propulsion efficiencies of these vehicles. Whilst the external structure of AUV platforms is relatively well-defined and hydrodynamically optimized, one area has seen limited focus and optimization. This is the immediate surroundings of the propulsion geometry and housing. In this body of work, we propose an adaptation to the traditional through-body tunnel thruster geometry of an over-actuated AUV platform. The modification is the inclusion of a retractable internal thruster cover. Subsequently, a comparison is provided between a clean-hull AUV configuration, one with open through-body thrusters, and one fitted with the designed cover geometry. A comprehensive computational fluid dynamics analysis is then converged and assessed using the Reynolds-Averaged Navier–Stokes equations. The drag and local flow fields are determined, where the covers are found to reduce the drag coefficient and total drag of the AUV by 9.51%, primarily due to a reduction of 9.91% in the pressure drag. These findings highlight the increased operational efficiency of the cover geometry and support the adoption of such covers for energy-constrained AUVs.