Medellín is a region where opportunities have been identified to improve the system for managing hazardous hospital waste (HHW). This study combines research methods of administration, environmental engineering, and public health, to assess the quality of these systems in eight out of 12 tertiary hospitals of the study region. These hospitals were used to model the process and propose an administrative tool to intervene its quality. Thereby, we applied a process checklist to audit compliance with current legislation, we conducted participant observation to understand the steps and relationships of the process, and we interviewed critical actors and analysed administrative practices to understand decision making and stakeholder involvement. Results included a digital model and the identification of four key factors such as: infrastructure, logistics management, administration, and managerial control. The hospitals certified the utility of these results to diagnose points of intervention, and to assess performance comparatively, which enhances opportunities for benchmarking.