This paper tries to identify and resolve ERP related problems at PT Mega Eltra, an Indonesian Small Medium Enterprise. Although PT Mega Eltra has implemented SAP ERP system for 3 years, several expectations are not met because the best practice implementation is not fulfilled. Thus, we apply soft system methodology to find the root cause of the current issues. We obtained data using interview to six employees. Then, we compare the best practice to the reality and identify the gap between them. Results show that PT Mega Eltra have problems in several aspects, namely project management, business process reengineering, vendor, strategy, training, and communication. We recommend several things to improve the business performance, such as upgrading server, automating third-party applications for approval, implementing customer relationship management and supply chain management systems, integrating HCM applications, implementing dashboard, and implementing knowledge management.