Single crystals of semi-organic potassium hydrogen phthalate crystals and l-proline(LP) amino acid (0.5 mol%)-doped potassium hydrogen phthalate crystals were implanted with 10 keV Ar⁺ ions at various fluencies of 1 × 10¹⁵, 5 × 10¹⁵, 1 × 10¹⁶, and 5 × 10¹⁶ ions/cm² to enhance their nonlinear optical property. Pure KHP, L-proline (0.5 mol%), and Ar⁺ ion-irradiated samples were characterized by single-crystal X-ray diffraction, powder X-ray diffraction, UV–visible spectroscopy, photo luminescence spectroscopy, microhardness testing, dielectric study, and non-linear optical (NLO) behavior. The study reveals that the Ar⁺ ion irradiation led to physical and chemical changes which altered the mechanical and optical properties of the samples. The l-proline-doped KHP showed an improved second-harmonic generation (SHG) efficiency compared to the KHP Ar⁺ ion-irradiated crystals. The energy deposition by the ion beam in the sample was studied by simulations using SRIM-2013 program. The study reveals that the Ar⁺ ion irradiation indicated the role of defects which could have influenced the non-linear optical behavior. Theoretical values of SHG calculated using the Python computational package indicate that further increase of Ar⁺ ion fluence will increase the SHG in l-proline (0.5 mol%)-doped KHP crystal. Further, it was prognosticated that beyond the Ar⁺ ion fluence of 1.9 × 10¹⁷ ions/cm², the crystal size diminished.