Microwave-assisted induction heating (MAIH) is a complex heating process characterized by rapid and uniform heating based on a combination of microwave heating (power: 1000 W; frequency: 2450 MHz) applied from above and electromagnetic induction heating (power: 1500 W) applied from below. In this study, we assessed the utility of MAIH in processing the flesh of barramundi (Lates calcarifer), an important aquaculture species in Asian countries. To determine the effects of different heating conditions on the microbial contamination and physicochemical qualities of barramundi meat, fresh barramundi meats (100 g) were sealed in heat-resistant crystallized polyethylene terephthalate containers containing 150 mL of saline solution, and were subsequently heated in MAIH to 90 °C or 70 °C and held to different time. The results revealed that in response to an increase in the duration of heating, there were reductions in the aerobic plate count, psychrotrophic bacteria count, hydrogen sulphide-producing bacteria count, and coliform count, along with lower contents of total volatile basic nitrogen, in treated samples. Conversely, with a prolongation of the time exposed to heat, we detected increases in the L* (lightness),W (whiteness), ΔE(colour difference), and texture (hardness and chewiness) of fish meat, whereas there was a reduction of a* (redness). When the samples were heated for at least 110 s to 90 °C or for at least 130 s to 70 °C, the barramundi meats obtained appeared to be fully cooked with microbial counts below the limits of detection. In addition, under both heating conditions, thermal imaging revealed a uniform distribution of temperature within treated samples. Furthermore, monitoring of temperature profiles at central points in fish samples revealed that maximum temperatures of 97 °C and 79 °C were reached in response to MAIH processing at 90 °C for 110 s and 70 °C for 130 s, respectively. Thus, on the basis of the quality considerations of appearance, microbial count, and texture, the recommended optimal heating conditions for barramundi meats produced using MAIH are 90 °C for 110 s and 70 °C for 130 s. Industrial relevanceThe MAIH equipment is a novel thermal processing technology and allows food to be heated and pasteurized simultaneously after the package is sealed, eliminates issues of secondary contamination due to the need for subsequent packaging, and extends the shelf life. MAIH technology, therefore, serves as a viable future alternative for thermal processing of manufacturing refrigerated ready-to-eat seafood.