Organic heterocyclic compounds having nonlinear optical behavior such as N-(1H-benzimidazol-2-yl) benzamide [2-BIBA], N-(1H-benzimidazol-2-yl)-2-methoxybenzamide [2-BIMBA] and N-(1H-benzimidazol-2-yl)-2-fluorobenzamide [2-BIFBA] were synthesized by benzoylation of 2-aminobenzimidazole using substituted benzoylchlorides. GC-MS was employed to validate the molecular ion peaks at 237, 268 and 255 for the synthesized molecules 2-BIBA, 2-BIMBA, and 2-BIFBA. Single crystal X-ray diffraction studies on grown single crystals demonstrate that 2-BIBA and 2-BIFBA were monoclinic systems exhibiting space groups C2/c and P2₁/c, respectively. In addition, 2-BIMBA as a triclinic system has the P-1 space group. The crystallinity of title molecules was optimised, and all theoretical investigations were done by B3LYP/6–311 + +G (d, p) basis collection and density functional theory (DFT). The obtained crystals are stable up to 423 K, 433 K, and 353 K for 2-BIBA, 2-BIMBA & 2-BIFBA, respectively, as demonstrated by TGA and DTA studies. Kurtz- Perry powder approach confirmed SHG for 2-BIBA, 2-BIMBA, and 2-BIFBA crystals, with SHG efficiency 2.07, 3.30, and 2.68 times larger than KDP. By adopting the zone of inhibition method, the antibacterial and antifungal properties of the single crystals generated were tested with ciprofloxacin and amphotericin-B as standards.