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Micellar casein concentrate (MCC) is a novel dairy ingredient with high protein content. However, its poor functional properties impair its potential for further application, highlighting the importance of using innovative processing methods to produce modified MCC, such as ultrasound (US). This work investigated the impact of US on the physical and functional properties of MCC under temperature-controlled and -uncontrolled conditions for different time intervals. Under temperature-controlled ultrasound (TC-US) treatment, a reduction was found in the supernatant particle size of casein micelles. Soluble calcium content and hydrophobicity increased following ultrasound treatment at 20 °C, resulting in a remarkable improvement in emulsification. However, long-time ultrasonication led to an unstable state, causing the MCC solutions to show shear thinning behavior (pseudoplastic fluid). Compared with 50 °C temperature-controlled ultrasonication, ultrasonication at 20 °C had a greater influence on particle size, viscosity and hydrophobicity. These findings indicate that 20 °C TC-US could be a promising technology for the modification of MCC.