Smoking in Nigeria is the most affordable and widely used traditional fish processing method aimed at preserving or reducing losses. However, smoked fish can be a source of microbial hazard. This study assessed the biophysicochemical changes of fish muscles along the processing line of Oreochromis niloticus
in Eleyele lake. A Structured questionnaire was administered to the fish processors in order to identify the procedural processing line of their fish. Microbial assay was done for total aerobic bacteria, enterobacteriacea, and salmonella counts. Nine processing stages identified in fish processing include: Stage 1- unwashed fish muscle tissue; Stage II- washed fish muscle tissue (washed, scalded, eviscerated and washed again); Stage III- Salted fish at 28.90° C; Stage IV- Salted Fish in the smoking kiln after 30 minutes at 75° C (temperature of smoking flame); Stage V - Salted fish in the smoking kiln after 1hr at 76° C; Stage VI- Salted fish in the smoking kiln after 1hr 30min. 65° C; Stage VII- Salted fish in the smoking kiln after 2hr at 40° C; Stage VIII -Salted fish in basket after 24hrs of storage; and Stage IX- Salted fish in basket after 48hrs of storage at 26-28° C ambient temperature. A significant increase (P<0.05) was recorded in total aerobic plate count (TAPCs) from stage I (7.42CFU/g) to II (12.00CFU/g) when the tilapia fish was washed using the water from the lake, scalded and eviscerated. The reverse was the case with the enterobacteriaea counts (EC). At stage III, where salt was sprinkled on the fish, a significant decrease (P<0.05) was observed in the TAPCs from 12.00±0.00CFU/g to 9.17±3.22CFU/g. Also, a significant decrease (P<0.05) was observed in all the counts in the first 30 minutes of smoking (stage IV) when the temperature rose from 28.9° C to 75° C. Furthermore, a significant decrease (P<0.05) was recorded only in the TAPC while a significant increase (P<0.05) was observed in EC and Salmonella counts. A significant increase in TAPCs was observed during storage from 7.56 ±0.10CFU/g (stage 7) to 12.0±0.00CFU/g (stage 8) while a significant increase (P<0.05) was observed in ECs from stage 8 to 9. Significant differences (P<0.05) were obtained for zinc, manganese, iron along the processing line, but Lead, Cadmium, Chromium, Nickel and Copper showed no significant differences. This study showed significant changes in the biological, physical and chemical changes of fish muscles along the processing line of Tilapia. The implications and public health concerns are hereby discussed.