Two mononuclear complexes [Co(LI)2] (1) and [Co(LII)3] (2) (HLI = N-cyclohexyl-3-methoxysalicylideneimine, HLII = N-cyclohexyl-3-ethoxysalicylideneimine) are reported. Although both compounds were obtained using the same synthetic procedure, 1 contains Co(II), while 2 is a Co(III) complex. The crystal structure of 1 was found to be the same as reported recently in the literature, while the crystal structure of 2 was established herein for the first time. The ligands in 1 are trans-1,5-N,O-coordinated, yielding a square planar CoN2O2 coordination core, while complex 2 adopts a meridinal isomeric form with both Δ and Λ configurations (Δ-mer-2 and Λ-mer-2). Optical properties of 1 and 2 were studied by the means of UV–vis spectroscopy in CH2Cl2 and MeOH. Both compounds absorb, mainly, in the UV region due to intraligand transitions and a ligand-to-metal charge transfer. The absorption spectra of both complexes also revealed two low intense bands at about 550 and 650 nm, which were attributed to d–d transitions. Molecular docking was applied to probe 1, Δ-mer-2 and Λ-mer-2 toward a series of the SARS-CoV-2 proteins. Both 1 and 2 are active against all the applied proteins; however, 1 is significantly more efficient with the docking scores being either comparable to or even higher of those of the initial ligands. The best binding affinity for 1 was established for PLpro, Mpro and Nsp3_range 207–379-MES. For both isomers of 2, the best binding scores were revealed with Nsp16_GTA site, PLpro, and Nsp3_range 207–379-MES (for Δ-mer-2) and Nsp16_SAM site (for Λ-mer-2). Ligand efficiency scores for the initial ligands as well as complexes 1 and 2 inside the binding sites of the applied proteins were also calculated. Of all complexes, the ligand efficiency scores for complexes of 1 with PLpro and Mpro are within the recommended ranges for a Hit, and the obtained ligand efficiency scores for complexes PLpro–1 and Mpro–1 are superior to those for the initial ligands.