The vannamei shrimp (Litopenaeus vannamei) is a high-value fishery commodity widely consumed due to its economic and nutritional benefits. This study evaluated the microbiological quality of fresh vannamei shrimp sold in three modern markets in Makassar City based on total plate count (TPC) and addressing Escherichia coli, Salmonella, and Vibrio cholerae, while analyzing the relationship with operational aspects of distribution and handling. Samples were collected from three modern markets and were analyzed in the Central Laboratory for Fisheries Product Quality Control, South Sulawesi Province. The results indicated that TPC values ranged from 1.4 × 10⁵ to 9.4 × 10⁵ CFU/g, with several samples exceeding the maximum limit of 5.0 × 10⁵ CFU/g, as defined by the Indonesian National Standard (SNI 01-2728.1-2018), indicating that some shrimp samples did not meet microbiological safety standards. E. coli contamination was found to exceed the safe limit in samples from Market B (23, 9.2, and 14 MPN/g), while samples from Markets A and C remained within acceptable limits (<3 MPN/g). Salmonella was detected only in Market B, whereas Vibrio cholerae was present in all samples. Operational factors such as transport distance (4.4–14km), supply frequency (1–7 times per week), and storage practices during sale contributed to the variation in microbial contamination levels. These findings highlight the need for improved monitoring of the shrimp distribution chain, better handling practices, and stricter hygiene protocols to ensure the safety and quality of the vannamei shrimp sold in modern markets in Makassar.