GC-EIMS analysis, antifungal- and anti-aflatoxigenic activities of the ethanolic extract of Capsicum chinense and Piper nigrum fruits and their main bioactive compounds were evaluated upon Aspergillus parasiticus. The GC-EIMS analysis showed capsaicin (50.49%) and piperine (95.94%) as the major constituents in C. chinense and P. nigrum, respectively. MIC50 values revealed that capsaicin (39 μg/mL) and piperine (67 μg/mL) were lower than those from fruit extracts of C. chinense (381 μg/mL) and P. nigrum (68 μg/mL). Extracts and bioactive compounds showed anti-aflatoxigenic activity. Maximum aflatoxin inhibition occurred at 150 µg/mL of extracts and compounds. The present study showed satisfactory results concerning the effects of ethanolic extract of C. chinense and P. nigrum fruits upon A. parasiticus, showing the capabilities of inhibiting fungal growth development and altering aflatoxins production.