We present a computational analysis of the complex proton-transfer processes in two protic ionic liquids based on phosphorylated amino acid anions. The structure and the short time dynamics have been analyzed via ab initio and semi-empirical molecular dynamics. Given the presence of mobile protons on the side chain, such ionic liquids may represent a viable prototype of highly conductive ionic mediums. The results of our simulations are not entirely satisfactory in this respect. Our results indicate that conduction in these liquids may be limited due to a quick quenching of the proton-transfer processes. In particular, we have found that, while proton migration does occur on very short timescales, the amino groups act as proton scavengers preventing an efficient proton migration. Despite their limits as conductive mediums, we show that these ionic liquids possess an unconventional microscopic structure, where the anionic component is made by amino acid anions that the aforementioned proton transfer has transformed into zwitterionic isomers. This unusual chemical structure is relevant because of the recent use of amino acid-based ionic liquids, such as CO2 absorbent.