Older adults often experience serious problems in spatial navigation, and alterations in underlying brain structures are among the first indicators for a progression to neurodegenerative diseases. Studies investigating the neural mechanisms of spatial navigation and its changes across the adult lifespan are increasingly using virtual reality (VR) paradigms. VR offers major benefits in terms of ecological validity, experimental control and options to track behavioral responses. However, navigation in the real world differs from navigation in VR in several aspects. In addition, the importance of body-based or visual cues for navigation varies between animal species. Incongruences between sensory and motor input in VR might consequently affect their performance to a different degree. After discussing the specifics of using VR in spatial navigation research across species, we outline several challenges when investigating age-related deficits in spatial navigation with the help of VR. In addition, we discuss ways to reduce their impact, together with the possibilities VR offers for improving navigational abilities in older adults.