L-Histidine malonate is one of the potential organic material for nonlinear optical applications. Single crystals of l-Histidine malonate were grown by the liquid diffusion method. The lattice parameter values were evaluated from single crystal X-ray diffraction technique. The Fourier Transform Infra Red and Raman spectral studies were employed to identify the different modes of vibrations of molecular groups in the crystal. Optical characterization and the percentage of optical transmission were recorded using UV–vis–NIR spectroscopy. The molecular structure was established by proton and carbon Nuclear magnetic resonance spectral studies. The thermal behavior of the material has been studied by Thermo gravimetric and Differential thermal plots. The second harmonic generation conversion efficiency was found out from the powder technique of Kurtz and Perry.