Magnetic microrobots and nanoparticles offer unique capabilities for medical applications by granting unprecedented access to intricate and delicate anatomical structures. Nevertheless, an intuitive manipulation approach remains a challenge due to their small size and limited feedback. This study presents a new method for magnetic microrobot and nanoparticle control that employs virtual reality (VR), creating an immersive and realistic view of the bodily anatomy and the microrobot within. This study compares three manipulation modes: a traditional mode using 2D displays, VR mode using a VR headset and touch controllers, and VR autonomous programmed maneuvering. It is shown that VR‐assisted modes reduce the manipulation time by improving spatial awareness. Nanoparticles in a VR environment are also manipulated. The proposed method will find applications in terms of intuitive, immersive microrobots or magnetic nanoparticle control in complex biological environments, thus in many medical procedures and for drug and cell delivery. The immersive nature of this approach enhances the ability of the user to perceive and understand complex anatomical structures, facilitating better navigation within delicate environments; both dexterity and spatial awareness are improved. Thus, it is shown how microrobots and magnetic nanoparticles can be controlled using immersive simulations to improve both visualization and manipulation.