Synthesis of new Fe(III), Co(II), Ni(II), and Cu(II) complexes of two azo ligands; 1-(phenyldiazenyl) naphthalene-2-ol (sudan orange R, HL¹), and sodium 2-hydroxy-5-[(E)-(4-nitrophenyl) diazenyl]benzoate (alizarin yellow GG, HL²) have been reported. Stoichiometries of 1:2 and 1:3 (M:L) of the synthesized complexes were approved by total-reflection X-ray fluorescence technique (TXRF) and by elemental analyses. The geometry of complexes (octahedral and square planar) was typified by various spectroscopic, thermal, and magnetic techniques. The ESR spectroscopy showed that Cu(II) complexes are of different isotropic and rhombic symmetries with the existence of Cu–Cu ions interaction. TGA, DTA, and DSC analyses supported the multi-stage thermal decomposition mechanisms, where the thermal breakdown is ended by the formation of metal oxide in most cases. Moreover, chemical reactivity modeling using the density functional theory (DFT) method with the B3LYP/6–31 basis set, showed that metal complexes are more biologically active than their precursor ligands. The calculated lipophilicity character for metal complexes is in the range of 33.8–37.5 eV. Docking results revealed high scoring energy for [Fe(HL²)₃].H₂O complex and moderate inhibition strength of [Cu(L¹)₂].H₂O complex versus 1bqb, 3t88, and 4esw proteins. Ultimately, the extent of biological effectiveness was endorsed experimentally against four microbial strains. The results are guidelines for toxicological investigations.