N-methylcytisine alkaloid was fully characterised by FTIR and ultraviolet spectroscopies. Two structures of this alkaloid that change the position of carbonyl groups, called C1 and C2, were theoretically analysed in both the gas phase and water solution at the B3LYP/6-311++G** level of theory. The dipole moment values of this molecule increase in the solution. The structural properties of N-methylcytisine were analysed to investigate its conformational preference given in natural sources. Then, Mulliken, MK and NPA charges with bond orders, natural bond orbital, molecular electrostatic potentials and topological properties expose a higher stability of this molecule in water solution. The frontier orbital analysis justifies the blue and red colourations observed in the mapped surfaces corresponding to electron density. Very good agreements with experimental data are observed for C2 in both H-1- and C-13-NMR spectra and their presence was supported by the ultraviolet spectra. For the first time, a complete assignment of infrared bands and force constants of N-methylcytisine in both media are reported as the scaled frequencies are in agreement with those experimentals. Molecular docking studies were used to predict the biological activity, which evidenced that N-methylcytisine alkaloid can act as partial agonist of nicotinic acetylcholine receptors.