The thermal phase transitions and physicochemical properties of a series of 21 amino acid-derived protic ionic liquids and four protic molten salts have been investigated. Structure–property comparisons for this series were investigated for alkyl- and cyclic amino acid cations, and ethoxy and methoxy groups on the cation, combined with nitrate or various carboxylate-containing anions. All the protic fused salts were found to be ‘fragile’. Most of the protic fused salts exhibited a glass transition, with the transition temperatures ranging from –90° to –42°C. Viscosities and conductivities ranged from 0.03 to 15.46 Pa s and 0.02 to 2.20 mS cm–1 at 25°C respectively. The protic ionic liquids alanine methyl ester glycolate, proline methyl ester nitrate, and proline methyl ester glycolate were found to be capable of supporting amphiphile self-assembly. Lamellar or hexagonal liquid crystalline phases were observed with the cationic surfactant hexadecyltrimethylammonium bromide and the non-ionic surfactant Myverol 18–99K.