The aim of this study was to develop an effective integrated cultivation system for Haematococcus pluvialis as a source of bioactive compounds such as astaxanthin, lutein, proteins, and fatty acids (FAs). The Chlorophyta H. pluvialis was cultivated in a vertical bubble column photobioreactor (VBC-PBR) under batch mode, allowing switching from green to red phase for astaxanthin induction. The combined effect of light intensity and nutrients on bioactive compound formation was investigated. Results showed that growth under lower nutrients availability and light intensity led to a higher concentration of biomass. Growth under high light intensity with an appropriate concentration of nitrate, sulfate, phosphate and magnesium led to ~85% and ~58% higher production of total carotenoids and fatty acids, respectively. Under high stress conditions, ~90% nitrate and phosphate consumption were observed.