Managers must regularly make decisions on how to access and deploy their limited resources in order to build organizational capabilities for a sustainable competitive advantage. However, failure to recognize that organizational capabilities involve complex and intricately woven underlying processes may lead to an incomplete understanding of how capabilities affect competitive advantage. As a means of understanding this underlying complexity, we discuss how managerial decisions on resource acquisition and deployment influence capability embeddedness and argue that capability embeddedness has an incremental effect on firm performance beyond the effects from organizational resources and capabilities. To investigate these issues, we present a hierarchical composed error structure framework that relies on cross‐sectional data (and allows for generalizations to panel data). We demonstrate the framework in the context of retailing, where we show that the embeddedness of organizational capabilities influences retailer performance above and beyond the tangible and intangible resources and capabilities that a retailer possesses. Our results illustrate that understanding how resources and capabilities influence performance at different hierarchical levels within a firm can aid managers to make better decisions on how they can embed certain capabilities within the structural and social relationships within the firm. Moreover, understanding whether the underlying objectives of the capabilities that are being built and cultivated have convergent or divergent goals is critical, as it can influence the extent to which the embedded capabilities enhance firm performance.