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BACKGROUND: Red‐fleshed dragon fruit contains high amounts of heat‐sensitive betacyanin pigments that require non‐thermal technologies in their processing. Ultrafiltration (UF) can be a promising alternative technique for fruit juice clarification and cold sterilization. RESULTS: This study reported clarification of red‐fleshed dragon fruit juice by UF employing polyethersulfone UF membranes with pore sizes of 5, 10, and 20 kDa operated at three different transmembrane pressures of 1, 2 and 3 bar. Findings indicated that dragon fruit juice was best ultrafiltrated with the 10 kDa UF membrane at 3 bar, which resulted in the highest permeate flux (around 7.9 kg m⁻² h⁻¹), lowest retention of betacyanins (30.6%) and phenolic compounds (11.3%), as well as having the closest 2,2‐diphenyl‐2‐picrylhydrazyl hydrate scavenging ability as compared to that of the control. Resistance analyses presented that cake resistance (69–94%) played the major role in decreasing flux and was the dominant fouling cause in the UF process, while reversible (5–25%) and irreversible resistances (1–16%) had lesser impacts. Membrane characterizations using scanning electron microscopy and Fourier‐transform infrared spectroscopy suggested that the chemical structure and surface morphology of the UF membrane were hardly altered after being used and washed with detergents. Liquid chromatographic–mass spectroscopic analyses demonstrated that UF was successfully employed for juice clarification without affecting heat‐sensitive compounds of fruit juices such as betacyanins. CONCLUSION: Simultaneous selection of suitable membrane pore size and operation pressure is crucial for UF of fruit juice. UF is a promising technique in processing bioactive compound‐containing liquid foods. © 2021 Society of Chemical Industry