This paper presents a method for high-speed sample detection and position control in an electrostatic levitator. The algorithm uses images acquired from two charge coupled device cameras and allows for robust and reliable detection of the sample position under various process conditions. The results show improvements over position sensitive detector systems especially under harsh environments and during autonomous operation under microgravity conditions. The position of samples with a radius from 0.6 mm to 1.1 mm is detected in three dimensions with an accuracy of ±40 μm inside a 7 mm × 7 mm × 7 mm levitation area. The two orthogonally arranged cameras, recording images at a resolution of 260 px × 260 px, are used to calculate the position every 5 ms. The control model and the corresponding position controller for the three axes are presented as well. The system was successfully tested in the laboratory and under microgravity conditions at the drop tower, during parabolic flights, and on the MAPHEUS sounding rocket.