Bioactive compounds from vegetal sources are a potential source of natural biological activities. Therefore, this study aims to determine the polyphenolic compounds in chia (Salvia hispanica L.) seeds extract (CSE) and papaya (Carica papaya L.) seeds extract (PSE), and evaluate their antioxidant, antifungal, and anti-aflatoxigenic activities. The polyphenolic compounds of the ethanolic CSE and PSE were elucidated. Each of them was tested as antioxidant, antifungal, and anti-aflatoxins. The obtained data indicated that the chemical composition of chia and papaya seeds included 33.4 % and 18.4% of oil, 25.5 % and 31.5% of protein, and 12.4 % and 19.1 %of fiber respectively. CSE contained 9.55mg/g and 30.35 mg/g of phenolic compounds (PC) and flavonoid compounds (FC) respectively, while PSE contained 10.72 mg/g and 16.39 mg/g of PC and FC respectively. Both extracts exhibited the ability to scavenge the DPPH radical. However, it was noted that PSE was more efficient compared with CSE. In HPLC analysis, Ellagic acid and Vanillin were the major detected PC in CSE, while Caffeic and Chlorogenic acids were the major detected PC in PSE. On the other hand, both extracts reduced significantly the fungal growth and spore viability of all tested fungi and reduced the mycelial dry weight and aflatoxins production of Aspergillus parasiticus at all concentrations used compared with untreated control. Also, the reduction percentage was increased by increasing the concentration used. It can be concluded that CSE and PSE are potential sources of polyphenolic compounds with antioxidants, antifungal and anti-aflatoxigenic properties.