A method of coating a flexible substrate in a roll-to-roll deposition system is described. The method includes unwinding the flexible substrate from an unwinding roll, the flexible substrate having a first coating on a first main side thereof; measuring a lateral positioning of the first coating while guiding the flexible substrate to a coating drum; adjusting a lateral position of the flexible substrate on the coating drum depending on the measured lateral positioning of the first coating; and depositing a second coating on the flexible substrate, particularly on a second main side of the flexible substrate opposite the first main side. Further described is a vacuum deposition apparatus for conducting the methods described herein.