Background: The Functional Resonance Analysis Method (FRAM) analyses discrepancies between written protocols (Work-as-Imagined) and real-world practice (Work-as-Done) in healthcare. Work-as-Done is created based on multiple stakeholders, leading to variability in reported functions. No guidance exists how to manage this variability. This study examines between-stakeholder variation in Work-as-Done and its impact on differences from Work-as-Imagined in FRAM visualisations. Methods: Two FRAM studies were analysed: delirium diagnosis and treatment (1) and perioperative anticoagulant management in two hospitals (2). Heatmaps visualised between-stakeholder variability of reported functions in Work-as-Done. We assessed the impact of including only functions shared by multiple stakeholders on Work-as-Imagined versus Work-as-Done comparisons. Results: In study 1, 23 of 33 functions were shared among at least two stakeholders. In study 2, stakeholders shared 30 of 33 functions in Hospital 1 and 29 of 32 functions in Hospital 2. Including or excluding functions, e.g., only mentioned by one stakeholder, influenced the observed differences between Work-as-Imagined and Work-as-Done. Conclusions: Between-stakeholder variability in both studies influenced differences between Work-as-Imagined and Work-as-Done, which often is the starting point improving the process. Showing between-stakeholder variability in FRAM studies enhances transparency in researcher decision-making. This supports more informed analysis and discussion in process improvement efforts.