The Egyptian Mediterranean fisheries sector is a critical contributor to the country's economy, with fish exports amounting to approximately 40% of the country's total agricultural exports. The sector also plays a vital role in providing employment opportunities, particularly for those living along the Mediterranean coast. However, the sector has been facing various challenges that threaten its sustainability, including overfishing, illegal fishing practices, and environmental degradation. A value chain analysis can help to identify the various stages of the fisheries sector and their interdependencies. In this study, four value chain stages (vessels, wholesalers, retailers, and hypermarkets) were conducted in Alexandria, Egypt, for particular fish species (Mullus barbatus, Sardinella aurita, and Diplodus sargus). In order to conduct the value chain study in the sampling areas of small-scale fisheries, the following parameters were assessed in all fish samples: thiobarbituric acid (TBA), total volatile nitrogen (TVN), pH, and sensory freshness evaluation. The results of the TBA tests and TVN analysis revealed notable disparities between the groups. These tests were frequently used to estimate the quality and freshness of fish, and their findings showed that samples with higher concentrations of these substances had more failures. Conclusively, the current study recommends stricter regulations on harvest size restrictions, monitoring programs, certification procedures, postharvest facilities, seasonal closures, social enterprises, finance facilities, and habitat protection as suggested by applying value chain analysis in small-scale fisheries management.