The bursting of the “bubble economy” in 1989–1990 brought decades of challenge for Japanese Small and Medium-Sized Enterprises (SMEs), which had assumed the role of subcontractor within production networks dominated by large companies. This article explores the impact of a rapidly altered business environment, due to economic crisis, the decline of relational subcontracting, and technological change, on the management and organization of firms. It provides a needed historical account of Japanese SMEs striving to avoid “hollowing out,” and detailed case studies explain what gaining greater independence as a flexible specialist meant in practice. A focus on the immediate advantages of computerized tools could not bring about the intended strategic objectives, whereas the systemizing of new and existing resources in skills and equipment enabled sustainable competitive differentiation in production and products. The case studies map out the internal competence transformations of SMEs over time, and indicate the value of historical approaches to exploring strategic and organizational change.