A method for timing procedures in a microscope system, which has a plurality of microscope modules configured to carry out various processes, provision is made for a clock signal to be provided to all microscope modules by a central clock generator and for the clock signal to be modulated by a clock modulation circuit in order to produce a defined clock-pulse number. The microscope modules define a start time for carrying out a process by way of the clock-pulse number, carrying out the process as soon as the clock-pulse number is reached. Moreover, a corresponding microscope system is described.