The recent explosion of interest in the bioactivity of the flavonoids of microalgae is due to the potential health benefits of the polyphenolic components that are major dietary constituents. The present study focuses on the phytochemical screening and in silico studies of flavonoids. Total flavonoids content in Chlorella pyrenoidosa was estimated in two modes of cultivation (Autotrophic and Heterotrophic) and its implication in anti-proliferation and anti-inflammatory activity was assessed through in silico approach. H-Ras p21(PDB-4L9S) and Lipoxygenase (PDB-3V99) involved in proliferation pathway and inflammatory pathway were selected as the target proteins for in silico studies. Seven compounds were selected for molecular docking. Pharmacokinetic properties of these compounds were calculated using online tools and docking was performed using Auto Dock Vina. By comparing and analyzing their binding energies in Maestro Schrodinger, suite, it was observed that Epigallocatechin gallate exhibited least binding energy of −9.1 kcal/mol and hence has anti-inflammatory activity. Catechin has best binding affinity with H-Ras p21 and hence has anti proliferative activity. •In both the modes, aqueous extract yielded more phytochemicals (1.21 mg PE/mg of total phenols and 0.87 mg RE/mg dry cell weight of flavonoids) when compared to hexane and ethyl acetate extracts.•Chlorella pyrenoidosa, showed the presence of flavonoids caffeine, catechin, epicatechin, epigallocatechingallate,dihyroquerecetin-7,4′-dimethyl-ether,caffeoyl-d-Glucose and protocatechuic acid.•It was observed that Epigallocatechin gallate had the best binding energy (BE) indicating the best possible pose with a BE of −9.1 kcal/mol against the target molecule 3V99.