Qualitative methods are particularly well-suited to studying the complexities and contingencies that emerge in the development, preparation, and implementation of technological interventions in real-world clinical practice, and much remains to be done to use these methods to their full advantage. We aimed to analyze how qualitative methods have been used in health informatics research, focusing on objectives, populations studied, data collection, analysis methods, and fields of analytical origin. We conducted a scoping review of original, qualitative empirical research in JAMIA from its inception in 1994 to 2019. We queried PubMed to identify relevant articles, ultimately including and extracting data from 158 articles. The proportion of qualitative studies increased over time, constituting 4.2% of articles published in JAMIA overall. Studies overwhelmingly used interviews, observations, grounded theory, and thematic analysis. These articles used qualitative methods to analyze health informatics systems before, after, and separate from deployment. Providers have typically been the main focus of studies, but there has been an upward trend of articles focusing on healthcare consumers. While there has been a rich tradition of qualitative inquiry in JAMIA, its scope has been limited when compared with the range of qualitative methods used in other technology-oriented fields, such as human-computer interaction, computer-supported cooperative work, and science and technology studies. We recommend increased public funding for and adoption of a broader variety of qualitative methods by scholars, practitioners, and policy makers and an expansion of the variety of participants studied. This should lead to systems that are more responsive to practical needs, improving usability, safety, and outcomes.