A system and method for performing data-based optimization of performance indicators of process and manufacturing plants. The system consists of modules for collecting and merging data from industrial processing units, pre-processing the data to remove outliers and missingness. Further, the system generates customized outputs from data and identifies important variables that affect a given process performance indicator. The system also builds predictive models for key performance indicators comprising the important features and determines operating points for optimizing the key performance indicators with minimum user intervention. In particular, the system receives inputs from users on the key performance indicators to be optimized and notifies the users of outputs from various steps in the analysis that help the users to effectively manage the analysis and take appropriate operational decisions.