In the current research, our work measured the effect of silver nanoparticles (AgNP) synthesized from Larrea tridentata (Sessé and Moc. ex DC.) on the mycelial growth and morphological changes in mycelia from different phytopathogenic and beneficial fungi. The assessment was conducted in Petri dishes, with Potato-Dextrose-Agar (PDA) as the culture medium; the AgNP concentrations used were 0, 60, 90, and 120 ppm. Alternaria solani and Botrytis cinerea showed the maximum growth inhibition at 60 ppm (70.76% and 51.75%). Likewise, Macrophomina spp. required 120 ppm of AgNP to achieve 65.43%, while Fusarium oxisporum was less susceptible, reaching an inhibition of 39.04% at the same concentration. The effect of silver nanoparticles was inconspicuous in Pestalotia spp., Colletotrichum gloesporoides, Phytophthora cinnamomi, Beauveria bassiana, Metarhizium anisopliae, and Trichoderma viridae fungi. The changes observed in the morphology of the fungi treated with nanoparticles were loss of definition, turgidity, and constriction sites that cause aggregations of mycelium, dispersion of spores, and reduced mycelium growth. AgNP could be a sustainable alternative to managing diseases caused by Alternaria solani and Macrophomina spp.