Management system standards are used by many organizations all over the world. Many companies also implement more than one management system standard. This study focuses on organizations which operate at least two ISO-based management systems and analyzes the approaches for implementing and operating of these systems. The authors firstly present empirical results based on a survey and secondly two case studies which are compared regarding their approaches. A special focus is being put on the integration aspect in the context of the high level structure of ISO-based management system standards. The result shows that most companies with more than one management system standard try to integrate the management systems making use of the Annex SL. Despite the given high level structure and main processes, there are many differences in the integration of the analyzed companies. On the basis of these findings the authors suggest improvements of Annex SL.