This case study presents an overview of the main steps and challenges encountered in a qualitative, longitudinal investigation of how companies reconfigure and innovate their business models. A business model describes how a company is concretely realizing its long-term strategy, describing the choices for creating, delivering, and capturing value. The fast-changing nature and the increasing complexity of current competitive environments require companies to spend considerable effort into developing new solutions—and therefore innovating their business models—to remain competitive and succeed in the creation of added value. The methods case highlights the importance and the issues in the choice of approaches in qualitative research involving a multiple case study and a longitudinal perspective. We describe the decisions, steps, problems, and lessons learned throughout the phases of (1) research setting and selection of cases, (2) data collection, and (3) data analysis. The case allows us to shed light on the practical challenges that researchers have to face when analyzing the process of business model innovation, such as choosing proper cases; collecting and analyzing rich, temporal, and unstructured data from different companies; and drawing valuable insights from their analysis.