Systematic molecular dynamics simulations are used to study the structure, dynamics and transport properties of the ionic liquids composed of the tetra-butylphosphonium ([TBP]+, or [P(C4H9)4]+) cation with six amino acid ([AA]−) anions. The structural features of these ionic liquids were characterized by calculating the partial site-site radial distribution functions, g(r), and computing the dihedral angle distribution of n-butyl side chains in the [TBP]+ cations. The dynamics of the ionic liquids are described by studying the velocity autocorrelation function (VACF) and the mean-square displacement (MSD) for the centers of mass of the ions at different temperatures. The ionic diffusion coefficients and the electrical conductivities were evaluated from both the Einstein and Green–Kubo methods. The cross-correlation terms in the electric-current autocorrelation functions, which are an indication of the ion pair correlations, are investigated. The cationic transference numbers were also estimated to study the contributions of the anions and cations to the transport of charge in these ionic liquids. We determined the role of the amino acid anion structures on the dynamical behavior and the transport coefficients of this family of ionic liquids. In general, the MSD and self-diffusion coefficients of the relatively heavier non-planar [TBP]+ cations are smaller than those of the lighter amino acid anions. Introducing polar functional groups (acid or amide) in the side chain of [AA]− decreases the diffusion coefficient and electrical conductivity of AAILs. The major factors for determining the magnitude of the transport coefficients are the chemical functionality and the length of the alkyl side chain of the [AA]− anion of these [TBP][AA] ionic liquids.