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As the level of analysis grows from the individual, to the team or group, to the organization, the research methods used has to evolve to manage the uncertainties brought on by size and scope. Software organizations provide a scenario that blends knowledge-intensive work with high velocities of change, making it possible to carry out insightful field research with shorter periods of immersion. While the nature of the problem being studied, significantly drives the choice of research design, our focus on understanding the sources of enterprise agility in software organizations lends itself to a process research design. Furthermore, the emphasis on generating theory led to using a combination of grounded theoretic methods and comparative case analysis. In this paper, we share the research approach developed, and provide examples of how the study was designed, the data collected, reduced and analyzed. We conclude with a set of six lessons learned that are applicable for engaging and collaborating with software organizations.