The management of supply chains of the agri-food sector has become a very complex structure. Product variety has decreased, changes in legislatives and quality management requirements have a high influence, international trade is much higher, consumer demands about product freshness and food quality is fluctuate and processors and retailers ask for the implementation of quality systems. This has resulted in individual changes in the process and organisation level of the enterprises and in order to keep the costs minimal. The focus of this paper will be a cost-benefit analysis for the implementation of quality management/assurance systems. Only a few studies with the focus on HACCP and food safety exists in the part of costs and benefits of quality systems in the agri-food industry. And an approach with an integrated accomplishment of quality systems is still not publicised. With the view on this additional aspect a decision support model was developed. This model presents the requirements of existent quality, environmental and occupational health standards and is a basic for a cost benefit model for special scenarios and individual solutions for enterprises.