In today's field of distributed software architectures there is a need for environments allowing the easy development of applications consisting of heterogeneous software modules and having various Quality of Service requirements (e.g., timeliness, availability or security). System customization using middleware-services is a promising solution to deal with the coexistence of multiple applications with different Quality of Service requirements. From the security point of view, the goal for system customization is to permit the interoperation among applications having different, possibly inconsistent security constraints. This paper demonstrates how the software architecture paradigm is beneficial for addressing security issues in distributed systems through system customization. The software architecture paradigm allows the application developer to abstractly specify security-related requirements. Then, our framework takes in charge the system customization to meet these requirements. The practical use of our approach is also addressed by discussing its integration in a configuration-based distributed programming environment.