Indazoles represent one of the most important heterocycles in drug molecules. Therefore, in the pursuit of potent biological agents, a series of ligands (HL1-HL4) and their corresponding transition metal complexes [M(L1-L4)2(H2O)2] were synthesized by the condensation reaction of 6-aminoindazole with various derivatives of salicylaldehyde. Further, the compounds underwent characterization through several physicochemical (TGA, powder XRD, SEM, EDAX) and spectroscopic techniques (FT-IR, UV–Vis, NMR, mass spectrometry, ESR). These techniques suggested hexacoordinated stereochemistry of the metal complexes, where ligands chelate via oxygen atom of phenolic ring, azomethine nitrogen and oxygen atom of water molecules in 1:2 (M:L) molar ratio. The thermal stability of the complexes was demonstrated by thermal analysis revealing three step decompositions leaving behind metal oxide as an end residue. The surface morphology of the ligands was distinct from metal complexes as revealed by SEM analysis, while mapping images demonstrated the simultaneously existence of the elements. While, to ascertain the nature of the obtained compounds (crystalline or amorphous), powder X-ray investigation was conducted by utilizing a wavelength of 1.54 Å. The compound’s antioxidant potential was assessed through DPPH assays and anti-inflammatory activity was evaluated using BSA denaturation inhibition assay, while their antimicrobial potential was evaluated against six microbial strains (E. coli, S. aureus, P. aeruginosa, B. subtilis, C. albicans, A. niger) by serial dilution approach. The performed biological evaluations revealed that the complexes are more efficient in controlling infectious ailment in comparison of ligands. HL2 (2) and its Cu(II), Zn(II) complexes (11, 12) exhibited potent antimicrobial activity (MIC value: 0.0047, 0.0048 µmol/mL against B. subtilis) and potent anti-inflammatory efficacy (IC50 value: 6.7 ± 0.044, 6.9 ± 0.036 µM). All the complexes exhibited potent antioxidant activity and their is enhancement in the activity of Schiff base ligands upon complexation, complex (19) demonstrated the greatest activity with IC50 value 2.1 ± 0.059. Additionally, the ADMET score provided a robust indication of the compounds’ drug-like behaviour. Furthermore, the biological effectiveness of the highly microbial potent ligand HL2 (2) and its complexes (9–12) was demonstrated through computational studies. The binding studies exposed that complexes (11, 12) exhibited lowest binding energy at −7.8, −7.9 kcal/mol. While, DFT study emphasized that complex (12) exhibits the highest electrophilicity index value (6.359), suggesting its affinity for binding with biological molecules and also revealed that complexes exhibit greater potency compared to the ligands and could potentially be utilized as drugs for combatting pathogen-induced malformations.