With the ubiquitous proliferation of electronic payment systems, data and application security has become more critical for financial operations. The Payment Card Industry Data Security Standard (PCI DSS) has been developed by the payment industry to provide a widely-applicable and definitive security compliance among all components in electronic payment infrastructure. However, the security impact of PCI DSS incompatibilities and relevant security assessment approaches for such cases are yet to be investigated in a comprehensive manner. Therefore, in this paper we present a security assessment framework for payment systems under PCI DSS incompatibilities. Moreover, we analyze a case study to evaluate our proposal and to provide some guidelines to security experts for assessment of PCI DSS compliance.