The impact of high pressure homogenisation (HPH) on physico-chemical, microstructural, and rheological properties of quinoa protein isolate (QPI) suspensions were studied. Individual protein bands kept unchanged with HPH treatment up to 50 MPa, as revealed by SDS-PAGE. After HPH treatment at 50 MPa, large protein aggregates were disrupted, and particle size was substantially reduced from ~8.2–0.5 µm. Concurrently, water solubility, emulsifying, and foaming capability were significantly enhanced. QPI molecules after HPH treatment became more flexible with increased surface hydrophobicity and absorbed at the air-water and oil-water interfaces faster, resulting in a more rapid decrease of surface tension and interfacial tension. The secondary structure of QPI proteins was not significantly altered after HPH treatment as probed by FTIR. All QPI suspensions formed weak gels after thermal treatment (85 °C, 30 min), and HPH treated QPI suspensions resulted in a stronger gel strength with a more compact and homogeneous protein network microstructure. These results show that HPH treatment could be an excellent processing technique to modify the physico-chemical, techno-functional, and microstructural properties of QPI suspensions.