New water-soluble Schiff base complexes with potential antimicrobial applications were successfully synthesized. A modification was made by adding a sulfonate group to the ligand to increase the ligand solubility in water. The Schiff base ligand was synthesized from a 4-aminoantipyrine compound with salicylaldehyde (L1) and salicylaldehyde-5-sodium sulfonate (L2), while the complex was synthesized using metal Co(II) with L1 (Co-L1) and L2 (Co-L2). Analysis and characterization were performed using a UV–Visible spectrophotometer, Fourier-transform infrared spectroscopy (FTIR), Nuclear magnetic resonance (NMR), Powder X-ray diffraction (XRD), magnetic susceptibility balance, and elemental analysis. All the ligands and complexes produced were crystalline, the geometry of the Co(II) complex is octahedral, and the ligand coordinates via the oxygen atom of the phenolic hydroxyl group and the nitrogen atom of the azomethine group. The sulfonate group causes the compounds L2 and Co-L2 to have greater solubility in water than L1 and Co-L2. The Density functional theory (DFT) results show that the presence of sulfonate groups causes the Co-L2 complex to have a larger dipole moment, is more reactive than Co-L1, and confirms its significant solubility in water. In addition, adding a sulfonate group also increases its antibacterial activity and is supported by molecular docking studies.