Whereas qualitative research methods have become increasingly popular in the broader social sciences, they remain less prominent in entrepreneurship, innovation, and technology research. In the face of increased complexity of empirical phenomena in these fields of research, we make the case for qualitative research methods as one valuable methodological option for researchers to gain a better understanding of complex phenomena. By unbundling the challenges that the empirical examination of complex phenomena imposes on researchers, we outline that qualitative research methods are particularly well-suited to cope with these challenges. To shed more light on how researchers may use qualitative data to draw theoretical inferences, we propose an analytical approach for the examination of complex phenomena that systematically discloses the inner logic of these phenomena in a step-wise process. In a case study of strategic innovation trajectories in haute cuisine restaurants, we illustrate how researchers may apply this analytical procedure ‘in practice.’ Our illustrative analysis indicates that, despite the severe challenges that researchers face when exploring complex phenomena, the proposed analytical procedure provides a practical and helpful guide for researchers to gain a better theoretical understanding of complex phenomena based on qualitative data.