Weeds decrease yield in crops through competition for water, nutrients, and light. Due to the circumstances mentioned above and the challenge of the emergence of herbicide-resistant weeds, developing sustainable alternatives becomes imperative. Plant extracts formulated into nano- and micro-encapsulates (NPs) emerge as a viable option for weed management. The objectives of this study were to identify phytochemical compounds within the ethanolic extracts of Carya illinoinensis, Ruta graveolens, and Solanum rostratum; determine their pre-emergence herbicidal activity on the indicator plants Sorghum bicolor and Phaseolus vulgaris; produce and characterize NPs with plant extracts; and assess their phytotoxicity under greenhouse conditions. The extracts were provided by Greencorp Biorganiks de México. Phytochemicals were identified through colorimetric assays and HPLC-MS, while pre-emergence tests were conducted in vitro, assessing concentrations of 12.5, 25, and 50% for each extract. NPs were synthesized using the ionotropic pre-gelation method, with size, zeta potential, and encapsulation efficiency (EE) being characterized. Finally, post-emergence tests were carried out in a greenhouse with seedlings. Compounds belonging to the hydroxycinnamic acid, flavonol, methoxyflavonol, hydroxybenzoic acid, methoxyflavone, tyrosol, stilbene, and lignan families were identified in all extracts. The pre-emergence herbicidal activity was observed for all extracts, with germination percentages ranging from 0 to 41% in both indicator plants. NPs exhibited sizes between 290 and 345 nm, zeta potentials ranging from −30 to −35 mV, and EE up to 94%. Finally, enhanced herbicidal activity was observed with plant extract NPs, with the species S. bicolor being more susceptible. NPs containing plant extracts are a viable option for bioherbicide production; however, continued research is necessary to refine formulations and enhance efficacy.