Good Clinical Laboratory Practices (GCLP) increase the quality and traceability of results in clinical research. However, high turnover of staff, insufficient resources, and lack of training in lab management may limit its implementation at Academic Health Centers (AHCs). This work aimed to qualitatively assess the staff perception of the implementation of a freeware Online Management System (OMS) on the workflow of an academic clinical research laboratory. A free online OMS (Quartzy, Quartzy Inc., USA) was selected and implemented from 2012-2016. After training interventions, a qualitative analysis was performed for the staff attitude towards the implementation, including a structured questionnaire (30 participants) and focus group assessments (16 participants). Indicators of management performance were also compared before and after the implementation. The results indicate that lab members perceive improvement in organization, communication, and commitment of staff, who reported the system as user-friendly and a facilitator for the autonomy of group members. On the other hand, there is a recognition of the need for constant training and engagement at the management level. These findings suggest that full-scope OMS may represent useful tools to assist in staff engagement in compliance with GCLP at AHC laboratories.