In the present study, theoretical harmonic vibrational frequencies (IR and Raman), carbon and proton NMR chemical shifts, geometric parameters, atomic charges (only for heteroatoms), reactivity indices (eLUMO, eHOMO, electronegativity, and hardness), and thermodynamical data (inner energy, enthalpy, Gibbs free energy, and entropy) of iminodiacetic acid (IDA) molecule have been investigated. We utilized ORCA software for B3LYP and HF (combined with Pople and Karlsruhe basis sets) calculations and MOPAC2016 software for semi-empirical calculations (AM1, PM3, and PM6). Theoretical vibrational frequencies and carbon and proton NMR chemical shifts have been compared with the corresponding experimental data. Although there was a strong correlation between the experimental and computational vibrational frequencies at low frequencies (<2200 cm−1), the computational predictions of vibrational frequencies were unsuccessful at high frequencies (>2200 cm−1). Distinctly, the studied computational approaches appeared to perform better in the prediction of carbon and proton NMR chemical shifts. Theoretical vibrational frequencies were also compared to each other to understand the impact of method choice (HF vs B3LYP D3 vs semi-empirical methods), dispersion correction (B3LYP D3 vs B3LYP), water solvation (SMD supplemented vs non-supplemented calculations), the family of basis set (Pople vs Karlsruhe basis sets), numbers of zeta (double vs triple zeta), polarization function (polarized vs nonpolarized basis sets), and diffusion function (diffusion supplemented vs non-supplemented basis sets). Moreover, geometric parameters, heteroatom charges, reactivity indices, and thermodynamical data produced by distinct computational approaches, as well, were compared to each other. Based on these comparisons, we detected critical factors (such as water solvation) acting on the computation of geometries, energies, and charges.