This study aimed to better understand the overall metabolic responses of Escherichia coli biofilms to the combined stresses of ultrasound and low concentration acidic electrolysed water (LcAEW, free available chlorine: 4 mg/L). The inactivation kinetics of all E. coli strains (ATCC 25922, ATCC 35150 and ATCC 43895) were simulated well by the modified Weibull model (R2: 0.81–0.97; RMSE: 0.04–0.71). By analysing metabolite profiles, ultrasound mainly disrupted nucleotide metabolism in E. coli cells within biofilms, as most intracellular nucleotide-related compounds (e.g., uridine, ATP, ADP) showed decreased trend especially in ATCC 25922 and ATCC 35150. Increased contents of most amino acids and decreased contents of most carbohydrates were shown in all strains after LcAEW treatment. Under combined treatment, adaptive strategies like glutamate decarboxylase system and mixed acid fermentation were activated to different extents among the three strains. These findings revealed that NMR-based metabolomics technology is promising in identifying strain-specific metabolic responses of biofilms to different antimicrobial treatments, providing guidance for future mechanism studies related to food contact surface sanitisation.