The purpose of this research is to study the challenges faced by organizations when implementing accounting software system in Malaysia. The focus of this research is on SMEs in Malaysia and the respondents are those involved in the implementation of accounting information systems in their companies. The small and medium enterprises (SMEs) are backbone for Malaysia’s economy. Hence, the SMEs’ successful business operations are significant to economic growth. The advantages of using business accounting software are the measurement of business results. The research uses questionnaires to collect data from the sample size of 102 managers and IT-staff in Malaysian SME whose companies implement accounting software system. The findings indicate that insufficient accounting skills and inadequate training present a significant impact on the implementation of accounting software system. Further, the lack of efficiency does not have any impact on the implementation of accounting software system in SMEs. Hence, it is concluded that insufficient accounting skills has a positive significant impact on the implementation of accounting software system. Finally, our research recommends to managers in conducting more training programs for their staffs who have insufficient capabilities and knowledge in their accounting and finance departments and to learn the basics in operating the accounting software system.