Protein isolates from six amaranth lines/cultivars (APIs) were evaluated to study their physicochemical (hunter colour, protein content and zeta potential), structural (thermal and conformational) and functional (emulsification, foaming, water and fat absorption) properties. APIs had protein content, whiteness index and gel temperature in range of 79.4–85.4%, 41.17–54.26 and 87.8–91.8 °C, respectively. The Fourier-transform infrared spectra of APIs revealed α-helix, β-sheets and random coil conformations in the secondary structure. APIs with higher relative proportion of β-sheets had higher Differential Scanning Calorimeter denaturation temperature and gel temperature. Minimum protein solubility (PS) was observed at pH 5.0, indicating isoelectric point (pI) of amaranth proteins. The PS, emulsifying activity index (EAI), emulsifying stability index (ESI), foaming capacity (FC) and foam stability (FS) of APIs at neutral pH were related to their zeta potential (ζ). The emulsifying and foaming properties were also determined at different pHs (between 2.0 and 9.0). The EAI-pH profile of APIs confirmed close relationship between the emulsifying ability and PS.