Amino acid choline-based ionic liquids (AACBILs) have high biodegradability, low toxicity, availability, low cost, and high thermal stability compared to the traditional ionic liquids (ILs). In this work, the volumetric, structural, and dynamical properties of three AACBILs, that is, choline alanine ([CH][Ala]), choline beta-alanine ([CH][beta-Ala]), and choline phenylalanine ([CH][Phe]) were investigated using the quantum mechanical calculations and also molecular dynamics simulations in both gas and liquid phases. The density functional theory calculations, noncovalent interactions, and also the quantum theory of atoms in molecules methods have been used to investigate the hydrogen bonds, interaction energies, and also charge transfers between the ions of the studied ILs. Density, isobaric expansion coefficient, mean square displacement (MSD), self-diffusivity, viscosity, electrical conductivity, and transference numbers have been computed for the studied AACBILs in different temperatures and at 0.1 MPa. There is a satisfactory agreement between the calculated data with the corresponding experimental values where they were available. Structural properties including radial distribution functions and spatial distribution functions of cations and anions were investigated. The results showed that because of the presence of an amine group away from the carboxylate group and also the absence of the planar phenyl group in the anion, the interactions between ionic pairs in [CH][beta-Ala] are stronger than interactions between ions in [CH][Ala] and [CH][Phe]. The results showed that the order of diffusions and electrical conductivities is [CH][Ala] > [CH][beta-Ala] > [CH][Phe], which can be interpreted by different electrostatic, van der Waals, and hydrogen interactions in these ILs. Our study provides considerable molecular insight into the structural features and dynamics of these biodegradable ILs.