Utilizing metal complexes to inhibit histone deacetylases (HDACs) and carbonic anhydrases (CAs) highlights their therapeutic potential, particularly in anticancer strategies. The metal complexes, with their unique three-dimensional structures, fit adequately into the active sites of the enzymes, not only improving selectivity but also providing facile coordination with amino acid residues to enhance their inhibitory ability. This review emphasizes the role of metal complexes in the selective inhibition of HDACs and CAs along with details of their mechanism of action. Additionally, we summarize the inhibition ability and cytotoxicity of metal complexes targeting HDACs and CAs, as well as the therapeutic implications that can lead to the invention and development of metal complexes as potent anticancer agents.