A method and system for controlled production of security documents, especially banknotes, wherein the security documents are subjected to a plurality of successive printing and processing operations on a plurality of processing stations. At least one production order is defined that may be subdivided into a plurality of production loads each being assigned a machine-readable load identifier. Selected processing stations are assigned to process the production order according to the production workflow. Each production load is selectively processed through the processing stations depending on the determined production workflow of the corresponding production order defined for each production load, whereby each production load is first subjected to a load acceptance procedure based on its machine-readable load identifier before being authorized to be processed on a selected processing station among the available processing stations.