•SFE as efficient method of flavonoids extraction from freeze-dried sprouts.•The best antibacterial activity the SFE extract from freeze-fried sprouts.•SFE of dried Lepidium sativum sprouts is efficient in extraction of isothiocyanates.•Water as efficient solvent for extraction of polyphenols from L. sativum seeds. The aim of this study was to evaluate chemical and biological potential of garden cress (Lepidium sativum L.) to receive valuable plant extracts with potential application in pharmacy or food industry. Four techniques of extraction and three environmentally friendly solvents such as water, supercritical CO2 and ethanol have been tested. Biological activity and chemical profile were evaluated in obtained extracts. GC/MS analysis showed that SFE extract from dried sprouts of L. sativum was especially rich in such glucosinolate derivatives as benzyl cyanide and benzyl thiocyanate. However, the extract obtained from freeze-dried sprouts by SFE with addition of 96% ethanol as co-solvent was especially rich in flavonoids and simultaneously exhibited the best antimicrobial activity. Comparison of MALDI-TOF-MS spectra of all obtained extracts clearly indicates that both SFE and maceration with water are the most selective techniques of extraction due to the lowest level of interfering substances with high molecular masses.