Masmin preparation is a traditional method that has been practiced for many years to preserve skipjack tuna (Katsuwonus pelamis) mainly in Lakshadweep. However, the method is not evaluated scientifically for its quality concerning nutrition and environmental contamination. Thus, in the present study tuna fillets from four stages of Masmin preparation, namely fresh, boiling, smoking, and sun-drying are evaluated for bacterial, nutritional, and heavy metal contents. The analysis revealed no significant difference in bacterial load, proximate nutrition (p = .93) and essential minerals, and heavy metals (p = .94) among all stages, suggesting the final product “Masmin” is nutritionally equivalent to the fresh tuna. However, pathogenic bacteria, such as Vibrio harveyi, Pseudomonas spp. Bacillus spp. are found, indicating poor hygiene during the processing. Heavy metals concentration like Al, Cd, Co, Cr, Mn, Ni, Zn, and Pb has increased with respect to previous reports, indicating an increase in pollution level in the catchment area that demands proper monitoring. Practical applications The findings inform the personnel engaged in Masmin preparation and consumption about the nutritional value of Masmin which is comparable to the fresh tuna even after different processing stages. Thus, the traditional fish preservation method could be applied to other economic important fishes where the cold facility is limited for fish preservation. On the basis of the microbiological analysis, we recommend the use of solar dryer and smokers in a traditional method of Masmin preparation to reduce microbial and dust contamination during processing and also it reduces the processing time that ultimately increases the production rate. Further, the findings from the heavy metal analysis bring into notice the increase in pollution level in Lakshadweep that raises health concern for the island populations and consumers.