A packaging process, apparatus and control system for articles to be packaged in box-shaped packagings are presented. The flow of box-shaped packagings and the flow of articles are efficiently managed, avoiding an excessive discarding of the box-shaped packagings during the process. Articles and open box-shaped packagings are conveyed in a continuous flow. Packaging compliance with the instructions related to the box-shaped packagings and article compliance with instructions related to the deposit of the articles are verified. Upon verification of the packaging compliance, the articles are transferred to the box-shaped packagings. In case of lack of packaging compliance, the flow of articles is suspended. In case of lack of article compliance, the articles to be transferred are moved to a buffer.