Salmonella is a leading cause of severe economic losses in poultry and foodborne illness in humans worldwide. The aim of this study was to determine the prevalence and multidrug resistance of Salmonella Enteritidis (S. Enteritidis) in several chicken abattoirs in Tripoli, Libya. The study includes the South, East, and West regions of Tripoli. Each region was assigned five slaughterhouses. Each chicken slaughterhouse was visited three times to collect samples. Five samples were taken at random from the neck skin, crop, and spleen. The total number of samples collected from all regions was 675. Bacterial isolation and identification, as well as antibiotic sensitivity testing, were performed on these samples. Salmonella spp. was found to be 15% prevalent, and S. Enteritidis was found to be 7% prevalent. The south region of Tripoli had the highest S. Enteritidis (9%), while the west region had the highest Salmonella spp. (22%). Salmonella prevalence increased significantly (p < 0.01) higher in the spleen (13%) as compared with the crop (5%) and neck (7%). Based on bacterial resistance pattern, Salmonella spp. isolated from the spleen had the highest multiple antibiotic resistance (MAR) index of 0.86 in the south region followed by MAR indexes of 0.8 and 0.46 in the West and East, respectively. Isolation of Salmonella from the spleen may indicate chickens' systemic infection and failure to control the most important microbe for public health. Thus, the control measures have to be revised and a national Salmonella control program should be put in place urgently.