The microbiome including fungi and bacteria secret biologically active secondary metabolites. Secondary metabolites have been recognized as a potential source of anticancer compounds. In this study, we reported the effect of some fungal and bacterial models secondary metabolites against Human lung cancer (A549), Human hepatocellular carcinoma (HepG2), and Human breast adenocarcinoma (MCF7). The evaluation of the anticancer effect is reported through cytotoxicity assay, which showed that viability and IC50 were concentration, cell type and metabolite dependent. Also, pathological examination showed variable effect on cellular content. GCMS report for the secondary metabolites for each microbiome. Aspergillus fumigatus and Aspergillus flavus were the most effective fungal strains in treatment of A549 cell line. Aspergillus terreus and Aspergillus fumigatus were the most effective fungal strains in treatment of HepG2 cell line. Aspergillus terreus and Aspergillus flavus were the most effective fungal strains in treatment of MCF7 cell line. Bacillus paramycoides was the most effective bacterial strain in treatment of A549, HepG2 and MCF7 cell lines. Histopathological changes detected under the effect of bacterial and fungal metabolites induced cellular and nuclear membrane irregularities, nuclear outlines and shrunked apoptotic bodies and peripheral chromatin condensation