Enterprise integration is the key enabler for transforming the collaboration among people, organization, and technology into an enterprise. Its most important objective is the transformation of a legacy operation into an e-enterprise. In an e-enterprise, the tight coupling between business process and the underlying information technology infrastructure amplifies the effect of hardware and software security failures. This accentuates the need for comprehensive security management of the infrastructure. In this chapter, the challenges posed by fulfilling myriad security requirements throughout the various stages of enterprise integration have been outlined. To better categorize these requirements, the set of security domains that comprise the security profile of the e-enterprise have been specified. The set of security metrics used to quantify various aspects of security for an e-enterprise are also identified. The chapter concludes by describing the details of the proposed security management strategy.