In the midst of rapidly changing business environment and technological advancement, ERP becomes the solution for companies to improve efficiency and effectiveness by integrating existing system thus that companies can increase their performance. Using RBV approach, companies can properly manage their resources through the organizational capabilities also play an important role in improving firm performance. This paper aims to examine the effect of ERP system implementation on firm performance both directly and indirectly through the organizational capabilities as intervening variable at manufacturing companies listed on Indonesia Stock Exchange period 2013-2017 which consists of 100 samples of ERP Adopters and Non-Adopters. The conceptual model in this study tested and analyzed using PLS-based SEM. The results showed that the implementation of ERP system has significant effect on firm performance and organizational capabilities. Organizational capabilities also have significant effect on firm performance. In addition, organizational capabilities have proven to mediate the relationship between ERP system and firm performance. This shows that the implementation of ERP system makes the information system to be integrated thus it enable companies to be more efficient and will affect the organizational capabilities in maximizing the utilization of company resources that ultimately can improve the firm performance.