The invention relates to a method for controlling the transport of sheets through a printing apparatus, in particular a digital printing apparatus. In the method for controlling the transport of sheets through a printing apparatus, a print queue is set by assigning images to respective sheets, prior to feeding the respective sheets into the transport arrangement. The sheets are then fed into the transport arrangement, and it is detecting whether a double sheet feeding has occurred. Superposed double sheets are deflected to a double sheet box, which is arranged upstream of the at least one print module, and at least those sheets following the superposed double sheet in the transport arrangement, for which an image has already been assigned and which are not in a duplex path, are guided to a waste box, which is arranged downstream of the at least one print module. Finally, the print queue is automatically reset and printing is continued without stopping the printing apparatus.