A method for the determination of cyanidin-3-glucoside (red kernel colour, RKC) in various matrices, including carbonated soft drinks, fruit-based soft drinks, sugar confectionery and milk-based drinks, by high performance liquid chromatography (HPLC) based on UV-Vis detection (at 520 nm) have been developed. Pre-treatment procedures for various matrices have been optimised. For soft drinks, the pH values were adjusted to 2.0, and sugar confectionery and milk-based drinks were extracted with 30 and 50% methanol in 0.1% formic acid (pH ~ 2.5) aqueous solutions, respectively. The limits of detection for the established methods ranged from 0.2 mg/kg for soft drinks to 2.0 mg/kg for the sugar confectionery and milk-based drinks with the relative standard deviations lower than 7%, which satisfy the method performance requirements for quality control for the beverages. The stability of the colourant RKC under various thermal and pH conditions was investigated by quadruple time-of-flight mass spectrometry (Q-TOF-MS). The main colourant component of RKC, cyanidin-3-glucoside (Cyd-3-Glu), lost the glucose entity under thermal treatment. A new component was identified when RKC degraded under various pH conditions and a degradation pathway is proposed. The results will assist in understanding the degradation mechanism of the colourant Cyd-3-Glu.