Previous results obtained in soybean–wheat rotations under no-tillage conditions showed reductions in the seedbank of the weed species Commelina benghalensis, but no alteration in the seedbank of Acanthospermum hispidum in areas infested with Brachiaria plantaginea. Analyses of the soluble fraction of B. plantaginea indicated the predominance of aconitic acid (AA) among the aliphatic acids and ferulic acid (FA) among the phenolic acids. Laboratory bioassays using C. benghalensis and A. hispidum were carried out to evaluate phytotoxic effects of pure organic acid solutions and dilute extracts of B. plantaginea on seed germination, root development, and fungal germination. Solutions of AA and FA were prepared at 0.25, 0.50, and 1.0 mM. Extracts of B. plantaginea were diluted to obtain concentrations of AA similar to those in the prepared solutions. Seeds were sown on 0.5% agar (containing AA, FA, or diluted extract) in plastic-covered receptacles and maintained in a germination chamber for 10 days. AA and FA solutions and the B. plantaginea extract reduced germination and root length, mainly of C. benghalensis. AA also stimulated the development of endophytic fungi (Fusarium solani), which had complementary adverse effects on C. benghalensis germination. FA and AA may play important roles in reducing the seedbank of some weed species, acting directly on germination and development and, indirectly, by stimulating endophytic fungi that alter germination.