Background Establishment of a systematic way of measurement and utilization of indicators for improvement is one of the most challenging issues in monitoring and evaluation of indicators in healthcare settings. In realizing these fundamental challenges, we designed a monitoring and evaluation system incorporating a hospital-wide quality variance report (QVR) system using linked Microsoft Excel® spreadsheets on Microsoft SharePoint®. Methods Indicators were determined at the departmental/unit level in line with the institutional goals, departmental functions, quality expectations, inputs/outputs, clinical priorities, compliance to policies/procedures/protocols/guidelines/pathways as well as in response to gaps in service delivery picked during root cause analyses. The sample design was determined in accordance with the characteristics of the population. Drawing of sample units was done using a simple random sampling technique without replacement or systematic random sampling. The indicator’s monitoring was enhanced visually by allocating colour codes based on performance across the months and quarters. The action plan tab consisted of a platform that aids in documenting corrective actions arising from the performance reviews. Results and discussion The QVR reporting system ensured a standardized format of monitoring throughout the institution with a reduced turnaround time from data collection to analysis. Further, continuity of the monitoring and evaluation (M&E) system was guaranteed even if an individual left the institution. The analysis of the QVR allowed hospital-wide trending on cross-cutting indicators with consequent ease of communication to multiple stakeholders. The automation has saved time and increased accuracy which has enhanced credible engagements during quality meetings. Conclusions Use of this system greatly enhanced quality performance monitoring in the hospital, identification of major bottlenecks that warranted hospital-wide projects or departmental-level projects. The QVR system enhanced the efficiency and accuracy of quality monitoring from data collection through to performance reviews. The QVR structure allows for customized development of an M&E database application software.