The economic crisis and the financial scandals highlight the significance of corporate governance. The internal audit function has gained great attention for assuring good corporate governance. ERP systems significantly change the information processing environment in organisations and act as a means of corporate governance change. ERP systems have embedded structures and institutional logics which could conflict with the corporate governance institutional logics in use. The internal audit function should be changed in terms of practices and structure to maintain its legitimacy as a corporate governance tool that adds value. In this paper, the authors articulate institutional theory to formulate a primary conceptual framework to explore how does the internal audit function respond to the misalignment between the ERP systems institutional logics and the corporate governance institutional logics. Internal auditors can respond to the misalignment with acquiescence, compromise, avoidance, defiance or manipulation strategies. This conceptual framework will be validated by conducting two case studies in Egypt and two in the UK in the banking sector.