The research subject was a method of integrating management systems in food sector enterprises. A planning phase as described in the PAS 99 specification was studied as one of the elements of the joint systems constituting an integrated management system. Four organizations were selected for the study, where at least two standardized management systems were introduced and certified. It was assumed that the investigated organizations should have an implemented HACCP system. The research study was a case study. In every organization, the employees responsible for the operation of management systems in the enterprise were interviewed. The study was performed in the form of in-depth interviews based on a predeveloped scheme according to the PAS 99 guidelines. Based on the research results, it was found that all the organizations surveyed were aware of the fact that in the case of emergency situations, risk management was a must. In three enterprises, the risk management procedures were implemented and in operation; in the fourth organization, the employees worked at implementing those procedures. In all the organizations, there was one person responsible for all the implemented management systems. The objectives linked with food safety constituted a minority compared to all other objectives adopted in the organization within the scope of management systems in operation therein. In addition, it was proved that the implementation of the system and the ISO 22000 certification did not cause any significant changes in the map of processes or in the type of actions taken by the organizations surveyed. Impediments to the integration of systems (including the planning element) were mainly associated with the fact that those organizations operated within international groups, where some rules were established top-down with no possibility to change them.