Micro-technologies based on wirelessly powered and manoeuvred submillimeter device, i.e., microrobots, are attracting growing attention. Their application in lab-on-a-chip systems, such as micromanipulation and in vitro cell sorting, is expected to steeply increase. However, the actuation, powering and control of microrobots are challenges that still need concrete solutions. Magnetic fields generally enable wireless navigation of microrobots, but proper control architectures and magnetic navigation systems are needed, depending on the specific task and on the level of interaction required to the user. Here we present a magnetic navigation platform intended for lab-on-a-chip applications and we address its usability with different levels of human involvement by using two control architectures: teleoperated and autonomous. We perform an experimental analysis to demonstrate that both architectures, enrolling different levels of interaction by the user, lead to reliable execution of the microrobotic task. First, we validate the open-loop response of the microrobotic system, and second, we evaluate the performance of the system by testing both control architectures with a standard mobility task. The results show that users can teleoperate the microrobot with 100% success rate, in 14.4 +/- 1.9s with a normalized spatial mean error of 0.60 +/- 0.13. Moreover, results show a fast decaying learning curve for the users involved in the study. Compared to this, when the navigation task is performed by the autonomous control, 100% success rate, a time of 8.0 +/- 0.5s and a normalized spatial mean error of 0.50 +/- 0.05 are obtained. Finally, we quantitatively demonstrate how both control methodologies enable very smooth movements of the microrobot, suggesting application for any task where repeatable and dexterous movements in liquid microenvironments are key requirements. Note to Practitioners-In life sciences, the need for advanced automation methods to sample preparation and analysis at the mi-croscale has increased at a steady pace together with microfluidic and lab-on-a-chip applications. Biological research especially requires new tools for cell micromanipulations since, to date, this is mostly achieved by manual handling by human operators. This has led to low manipulation efficiency and poor reproducibility. In such context, we developed a magnetic system for lab-on-a-chip applications that can be used for wirelessly manipulating a magnetic microrobot in a microfluidic environment. In this paper, we test its use as both a teleoperated and autonomous tool for navigating microrobots in a microfluidic environment with different levels of user interaction. The features of the magnetic system, such as its intrinsic simplicity, enable a reliable, natural and smooth motion of the microrobot through both control architectures. This leads to high performance and repeatability in automated tasks, as well as to exceptional intuitiveness in user-controlled tasks, as proven by the reported fast learning curve. We believe that this particular aspect will facilitate the adoption of this kind of magnetic navigation systems for a plethora of applications.