Staphylococcus aureus (S. aureus) is one of the most common zoonotic bacteria, which causes diseases and responsible for the development of resistance against various antibiotic agents. In Ethiopia, data about the pattern of S. aureus and its Methicillin resistant strain is limited. Therefore, the main aim of the current study was to provide the basic data on the detection of S. aureus, its Methicillin resistant strain and antibiogram assessment in Bahir Dar and Debre Markos municipal abattoirs. A cross-sectional study was conducted from January 2021 to April 2022. One hundred fifty swab samples were purposively collected from beef carcasses, knives, splitting axes, cutting tables, hooks, walls of the abattoir houses and personnel hands and cloths. Isolation and identification of S. aureus was performed according to ISO6888-2 and antibiogram assessment was conducted for ten selected antibiotic agents by the disk diffusion method based on Clinical and Laboratory Standards Institute guidelines. Conventional polymerase chain reaction was applied for the detection of mecA gene. S. aureus was detected as 25.3% (38/150) of the samples, out of which, 27.1%, 23.1%, and 26.9% from beef carcass, abattoir environment and abattoir workers, respectively. About 22.7% of S. aureus was isolated from Bahir Dar municipal abattoir, while 28% was from Debre Markos municipal abattoir. The highest proportion of S. aureus was detected from hands and hooks samples (35.7%), the lowest in the splitting axes (11.1%). Furthermore, the isolates were detected from knives, tables, walls and workers’ cloths with the proportion of 26.7%, 23.1%, 14.3% and 16.7%, respectively. All isolates were completely susceptible to Gentamicin; but 100% resistant were recorded to Penicillin and Methicillin. Around 84.2% of S. aureus isolates showed multi-drug resistance. Furthermore, the mecA gene was detected from five isolates (33.3%) of the 15 S. aureus isolates. The contamination of beef carcass, abattoir environment and abattoir workers with S. aureus may have significant risks on the public health and economic aspects in the study areas. Therefore, to minimize the risk of this pathogen, prevention and control strategies such as using most sensitive drugs, creating good abattoir hygiene, equipment and abattoir workers’ sanitation and good carcass handling were recommended.