The invention concerns the processing of value documents of different deposits using a value-document processing apparatus. Upon insertion of the value documents into the containers with which they are fed to the value-document processing apparatus, a beginning position and, where applicable, also an end position of the respective deposit is established for each deposit and transmitted to the value-document processing apparatus. Even in the case of different deposits in the same container, the invention enables an error-free association of the checked value documents with the different deposits. When a deposit comprises two separate sub-stacks that were inserted in the same or different containers, said sub-stacks of the contemplated deposit can be brought to account jointly and a joint rejects processing of the sub-stacks of the same deposit carried out.