Regular environmental monitoring (EM) system is indispensable routine activity in assessing the microbiological quality of the manufacturing environment surfaces for the production of medicinal products. However, the release of the full potential of such regular activity will not be achieved nor the elucidation for points of defects and improvements cannot be appropriately investigated unless systematic analysis of the results can be ensured and performed periodically. In the current study, statistical process control (SPC) and six sigma tools were used in the study of the quality of microbiological surface cleanliness in clean rooms in pharmaceutical manufacturing plant during ten months period on weekly basis using contact plates. Initial evaluation of data distribution showed that ten out of 11 partitions of the manufacturing area followed distributions other than the Gaussian ones which required logarithmic transformation to approach normalization for further statistical analysis. When control charts were constructed for transformed data, material followed by personnel airlocks showed the greatest risk of microbial excursions then the corridor with the overall risk of failure 99.5% suggesting that there was a state of significant imbalance between cleaning program and its frequency with the work type and load in these sections. The present work provided insight for the area of defects that could not be observed using conventional data trending and provided focus on defined sections that could impact the overall microbiological quality. This analysis provided a promising mean for designing quantitative risk assessment for microbiological quality control in pharmaceutical, human consumables manufacturing and other healthcare industries.