Background: The application of arbuscular mycorrhizal fungi (AMF) can induce the synthesis and accumulation of secondary metabolites in the tissues of host plants, thus impacting their allelopathic potential. Materials and methods: The objective of this study was to determine the effect of three AMF species (Rhizoglomus intraradices, Funneliformis mosseae, Rhizoglomus fasciculatum) on photosynthetic pigments and secondary metabolites content in roots and reproductive organs of Ipomoea purpurea L., Digitaria sanguinalis L., and Solanum nigrum L. as a problematic weed species. Results: Among compared weeds, the roots of D. sanguinalis associated with AMF accumulated the highest level of phenols. Higher content of flavonoids was obtained in roots of S. nigrum (7.46 mg g(-1) FW) following colonization with R. intraradices. Berries of S. nigrum inoculated with R. intraradices had a higher concentration of terpenoids (21.45 mg 100 mL(-1) of extract) than reproductive organs of D. sanguinalis and I. purpurea. Colonization with R. intraradices improved total phenolics in seeds of D. sanguinalis compared to the reproductive organs of other weeds. These compounds released from seeds help defend against pathogen infection, consequently increasing seed production. In addition, phenylalanine ammonia lyase enzyme activity in leaves of D. sanguinalis colonized by R. fasciculatum and F. mosseae was 55% and 67%, respectively, higher than I. purpurea plants, grown in the same condition.