Purpose: The aims of the study were to identify and evaluate the internal controls used in a computerized accounting system of the SMEs, to identify and evaluate the merits and demerits of the internal controls used in the companies, and to identify the challenges in the implementation of internal control systems in the computerized accounting system of the SMEs. Design/methodology/approach: The population of the study was the employees of the SME’s registered with Ministry of Commerce and Industry (MOCI) in Muscat, Oman. Samples were selected from this population on a random sampling basis. One-member employee from the SMEs representing the enterprise filled the questionnaire. The survey was conducted through a questionnaire using a Google form. 220 samples were collected from the population. The data collected was analyzed using data processing methods and Microsoft excel. Findings: The study found that SMEs were using computers to perform their daily transactions and the accounting software used by SMEs were cheap, of low quality and not proficient enough. One of the components of internal control system, i.e. monitoring was implemented by most of the SMEs and they also stated that they rarely hired an external auditor for auditing because of the expensive auditing fees. It was also stated that the security mechanisms were not properly implemented in the SMEs because of the expensive cost. Research limitations/implications: The study suggested that the Government should emphasize the SMEs to implement a good internal control system. This can reduce the errors and also increase the efficiency of operations. SOX in Omani context should be strictly implemented making it statutory and mandatory for all the SMEs in Oman and such statutory laws will help the auditors to abide by the rules and regulations to be followed. Social Implications : Government should support SMEs through providing education on the importance of internal control systems as most of the employees of SMEs are poorly educated/illiterates. The Government should set a price ceiling to the external auditors on the auditing fees exclusively for SMEs so that they can afford. Originality / Value: No study was carried before in relates to the impact of the internal control system through the computerized accounting system among the SMEs in Muscat, Oman. This study will through light on the statutory laws required for the sake of internal control measures required for the SMEs.