An in-package atmospheric dielectric barrier discharge cold plasma (CP) treatment integrated with malic acid (MA)-incorporated whey protein isolate coating treatment (MA-WPI + CP treatment) was developed to inactivate Salmonella and Listeria monocytogenes in steamed fish paste packaged in a plastic container. MA-WPI + CP treatment inactivated Salmonella and L. monocytogenes more effectively than either one of the treatments. MA-WPI + CP treatment more effectively inhibited the growth of Salmonella and L. monocytogenes in fish paste than MA-WPI coating during storage at 4 °C. The diffusion coefficients of MA in WPI films increased by CP treatment from 2.11 × 10−14 and 3.27 × 10−14 to 2.79 × 10−14 and 4.83 × 10−14 m2/s at 4 and 10 °C, respectively. The accelerated diffusion of MA by CP could increase the microbial inhibition in steamed fish paste coated with MA-WPI during storage. MA-WPI + CP treatment showed potential to increase microbial safety of steamed fish paste.