Service-oriented architectures are increasingly deployed in open, distributed and dynamic environments, which require an end-to-end security awareness security at each phase of the service’s lifecycle. Moreover, the security should not only focus on services without considering the risks and threats that might be caused by elements from business activities or underlying hardware and software infrastructure. In this paper, we adopt a holistic approach to define a security conceptual model that covers all elements at the business, service and infrastructure levels and guides each phase in a typical design method for service-oriented architectures. Since the information security is subject to uncertain and unforeseen threats, we propose a fuzzy logic decision system that helps identify security risks based on the security conceptual model and select appropriate security measures based on security objectives.