This study investigated the synergistic effect of combining flavourzyme, a natural enzyme, and floating electrode-dielectric barrier discharge (FE-DBD) plasma (1.1 kV, 43 kHz, N2 1.5 m/s) treatment, a non-thermal decontamination technology, against Escherichia coli biofilms in squid. E. coli (ATCC 35150 and ATCC 14301) biofilms were formed on the surface of squid and treated with different minimum inhibitory concentrations (MICs) of flavourzyme (1/8; 31.25 μL/mL, 1/4; 62.5 μL/mL, 2/4; 125 μL/mL, and 3/4 MIC; 250 μL/mL) and FE-DBD plasma (5, 10, 30, and 60 min). Independently, flavourzyme and FE-DBD plasma treatment decreased by 0.26-1.71 and 0.19-1.03 log CFU/cm2, respectively. The most effective synergistic combination against E. coli biofilms was observed at 3/4 MIC flavourzyme + 60 min FE-DBD plasma exposure, resulting in a reduction of 1.55 log CFU/cm2. Furthermore, the combined treatment exhibited higher efficacy in E. coli biofilm inactivation in squid compared to individual treatments. The pH values of the synergistic combinations were not significantly different from those of the untreated samples. The outcomes indicate that the combined treatment with flavourzyme and FE-DBD plasma can effectively provide effective control of E. coli biofilms without causing pH changes in squid. Therefore, our study suggests a new microbial control method for microbial safety in the seafood industry.