Excessive use of chemical herbicides has led to human health and environmental problems. However, environmentally friendly strategies for weed management are changing them competition in favor of crops. In this regard, the effects of different aqueous extract concentrations of root and shoot of black cumin on germination and initial growth of charlock mustard (Sinapis arvensis L.) and common wheat (Triticum aestivum L.) were compared in 2020 in the Agriculture Laboratory of the Faculty of Agriculture, Shahrekord University. The results showed that increasing the concentration of black cumin extracts increased hydrogen peroxide, lipid peroxide, and proline and decreased the germination parameters, mitotic index, cell viability, and vigor index of charlock mustard. Black cumin extract, even with the lowest concentration, restricted the vigor index of charlock mustard with a steeper slope than the wheat (18 and 4.5%, respectively). The presence of critical inhibitory compounds in black cumin extract, including polyphenols (such as tricarboxylic acids), flavonoids, and alkaloids (such as magnoflorine, myristicin, norargemonine, and nigellamine), restricts the germination indices of charlock mustard. Additionally, terpenoids such as cycloartenol, bisabolol, limonene, P-cymene, O-cymene, 1,8-cineole, myrcene, carvacrol, and thymol, which were higher in the shoot than the root, strengthen the inhibitory effects of black cumin extract. In general, due to the strong impact of black cumin extract on stopping the growth of charlock mustard weed and little impact on wheat seedlings, black cumin can be introduced as a viable candidate for natural herbicide production. In addition, its cultivation in rotation with a wheat crop, helps control charlock mustard and reduce the use of synthetic herbicides. Graphic abstract: [Figure not available: see fulltext.]. © 2023, The Author(s) under exclusive licence to Iranian Society of Environmentalists (IRSEN) and Science and Research Branch, Islamic Azad University.