We present a method to assess how aligned hospital information systems (HIS) are with quality standards adopted by the organization. Canonical action research is our mode of inquiry, in a district hospital implementing multiple certification standards. We build on the “ground-truth” provided by healthcare professionals to identify risks and opportunities for HIS developments while contributing to their awareness of its implications. We address different categories of design-reality gaps, namely the organizational, service, process, and individual. The findings suggest that HIS compliance should address five interrelated dimensions of context, people, processes, IT, and information/data. The proposed method allows self-evaluation through gap analysis and a comprehensive assessment of hospital quality, integrating HIS and healthcare processes. Moreover, it supports multiple quality models in hospitals and the development of heterogeneous HIS solutions in different maturity stages. HIS developments should be a priority for hospital quality worldwide; especially in the emerging economies that require methods accessible to their resources, standards compliance, and demographic demands for healthcare.