Choline amino acid ionic liquids have received much attention recently due to their environmental friendliness and low toxicity. Some of these ionic liquids have shown outstanding capacity for biomass and coal pretreatment, yet it remains unclear what structural features underpin performance. Despite sharing many structural features with other choline amino acid ionic liquids proven to be effective at lignin extraction, choline phenylalaninate (ChPhe) is surprisingly among the poorest solvents at such application. Using multi-contrast neutron diffraction we show that the liquid nanostructure of ChPhe – consisting of apolar domains in a continuous polar network – primarily consists of small clusters stabilised by inter-anion hydrogen bonds between amine and carboxylate groups. Within the apolar regions, phenyl side-chain rings adopt no preferred arrangements, signaling the absence of π-π stacking, but instead show evidence of competing cation-π interactions. This is the first example of self-assembled ionic liquid nanostructure not of solvophobic origin. The unusual suite of interactions also explains its water miscibility but inability to retain nanostructure upon water dilution, as well as its poor performance for biomass pretreatment, and provides a new strategy by which to engineer and tune ionic liquid nanostructure for the design of application-specific, renewable solvent systems.