The present study aimed to evaluate the antibiofilm effect of combined sonication treatment with organic acids on polystyrene surfaces and to develop a predictive model for the inactivation of Escherichia coli biofilms. Polystyrene plates containing E. coli biofilms were subjected to sonication using different inactivation solutions (PBS, lactic acid, and acetic acid) at varying temperatures (20 °C, 40 °C, and 50 °C) and durations (2 and 5 min). The effects of temperature, treatment duration, and inactivation solution on E. coli biofilm removal were statistically significant (p < 0.05). The use of organic acids, along with increased treatment time and temperature, led to a significant reduction in viable cell counts (0.43–6.21 log CFU/mL) and optical density (0.13–0.72 at OD600) of E. coli biofilms (p < 0.05). The highest E. coli biofilm inactivation, with a reduction of 6.21 CFU/mL and 0.72 OD, was achieved by combining organic acid and thermosonication at 50 °C for 5 min. A significant positive correlation was observed between test methods based on viable cell count and optical density (OD) measurements. According to multiple linear regression analysis results, the R2 values of the predictive models for biofilm inactivation, based on viable cell count and OD measurements, were 0.84 and 0.80, respectively. Due to its higher accuracy, the predictive model developed using viable cell count data is recommended for applications in the food industry and processing sectors.