The scientific community is exploiting the use of silver nanoparticles (AgNPs) in nanomedicine and other AgNPs combination like with biomaterials to reduce microbial contamination. In the field of nanomedicine and biomaterials, AgNPs are used as an antimicrobial agent. One of the most effective approaches for the production of AgNPs is green synthesis. Lysiloma acapulcensis (L. acapulcensis) is a perennial tree used in traditional medicine in Mexico. This tree contains abundant antimicrobial compounds. In the context of antimicrobial activity, the use of L. acapulcensis extracts can reduce silver to AgNPs and enhance its antimicrobial activity. In this work, we demonstrate such antimicrobial activity effect employing green synthesized AgNPs with L. acapulcensis. The FTIR and LC–MS results showed the presence of chemical groups that could act as either (i) reducing agents stabilizing the AgNPs or (ii) antimicrobial capping agents enhancing antimicrobial properties of AgNPs. The synthesized AgNPs with L. acapulcensis were crystalline with a spherical and quasi-spherical shape with diameters from 1.2 to 62 nm with an average size diameter of 5 nm. The disk diffusion method shows the magnitude of the susceptibility over four pathogenic microorganisms of clinical interest. The antimicrobial potency obtained was as follows: E. coli ≥ S. aureus ≥ P. aeruginosa > C. albicans. The results showed that green synthesized (biogenic) AgNPs possess higher antimicrobial potency than chemically produced AgNPs. The obtained results confirm a more significant antimicrobial effect of the biogenic AgNPs maintaining low-cytotoxicity than the AgNPs produced chemically.