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Uncertainty management is crucial for achieving high performance in enterprises that develop or operate complex engineering systems. This study focuses on flexibility as a means of managing uncertainties and builds upon real options analysis (ROA) that provides a foundation for quantifying the value of flexibility. ROA has found widespread applications ranging from strategic investments to product design. However, these applications are often isolated to specific domains. Furthermore, ROA is focused on valuation, rather than the identification of real options. In this paper, we introduce a framework for holistic consideration of real options in an enterprise context. First, to enable a holistic approach, we use a generalized enterprise architecture framework that considers eight views: strategy, policy, organization, process, product, service, knowledge, and information technology (IT). This expands upon the classical IT-centric view of enterprise architecture. Second, we characterize a real option as a mechanism and type. This characterization disambiguates among mechanisms that enable flexibility and types of flexibility to manage uncertainties. Third, we propose mapping of mechanisms and types to the enterprise architecture views. We leverage this mapping in an integrated real options framework and demonstrate its benefit over the traditional localized approach to ROA.