Pharmaceutical factory workers spend 37.5% of their daily time in the production hall manufacturing drugs used for human health needs. There is usually little or no time given to spend in the natural environment. This affects their sanity and well-being. The Pharmaceutical factory building (PFB) is classified as a specialized, controlled, or restrictive building; it provides little or no access to natural environmental conditions like ventilation and lighting, thereby increasing the financial implication of energy for the operation of production of drugs. Hence, the survey was conducted to identify the factors that influence the indoor environmental performance (IEP) of PFBs. The factors responsible for influencing the indoor air quality were measured through a survey conducted in Lagos and Ogun States, Nigeria on 14 PFBs to determine the value of these factors identified, using principal component analysis (PCA), Bartlett Test, and Kaiser-Mayer Olkin (KMO): the conditions for PCA were also observed. PCA is a factors or data reduction technique to select a subset of highly predictive factors from the larger group of factors identified from the study. Indoor environmental quality variables satisfied the condition for PCA while thermal performance variables did not meet the condition. PCA was conducted for Indoor environmental quality and the result showed 2 major factors explaining the variation in the original set of variables. Whereby CO2, P.M1.0, P.M2.5, P.M10, HCHO, airflow, AQICN, and AQIUS as component 1 and TVOC as component 2, the data set was also compared with the standards recommended for indoor environmental quality and thermal performance variables. It was found that at an average air velocity of 29°C and RH of 60%, the average CO, TVOC, PM2.5, and PM10 were 0.25ppm, 0.31ppm, 33.92ppm, and 43.48ppm respectively for the PFBs. Because thermal performance includes several dependent variables, greater research on the indoor environment of PFBs in Nigeria is recommended to determine the impact of indoor environmental characteristics on thermal parameters.