Audit is one of the control functions that signifies an assurance towards a company’s compliance with specific standards, guidelines and procedure in their operations, financials, people and activities. For entities that uphold the Shariah values and earns MS 1900:2014 certification from SIRIM Berhad, implementing good internal Shariah audit for quality management is one of commitments to achieve the compliance with the stated values. The commitment is significant and should be conducted yearly prior to the external process conducted by external auditors. However, there are challenges faced by the appointed internal auditor of MS 1900:2014 that may not be addressed and facilitated by the organization. This study explores challenges faced by MS 1900:2014 internal auditors. Focus group discussion (FGD) has been conducted with six respondents who have experience in conducting internal audit processes for more than two years. Findings show that the challenges faced by the respondents can be separated into three stages pre-audit, field audit and post audit process. Findings of this study can help the organization that earns the certification to come out with early preparation to facilitate the needs of their internal auditor team prior to the actual audit process.