In 2005, Malaysia crafted history as it instigated the first ever Islamic quality management system in the world, namely Islamic Quality Management System MS 1900:2005. MS 1900 is developed employing ISO 9001 as its base. MS 1900 is a structured system to help organisations in delivering products and services that congregate customers’ requirements, as well as regulatory requirements and the ... [Show full abstract] dictates of Shari’a (Islamic commandment). The Shari’a requirements are incorporated as an addition to the requirements of ISO 9001, and intend to close the gap that exists in the ISO 9001 standard in relation to the Islamic perspective. MS 1900 has three principles; namely compliance to the principles of Halal and Haram, value based management and decision taken in line with the objective of Shari’a (upholding human interest). Despite an ignition of interest in the promising of QMS in the recent years, little research has been carried out to study the MS 1900 implementation processes within higher education institutions. Little research has also been done to study what are the challenges involved in MS 1900 implementation within higher education environment. Therefore, the objective of this paper is to present challenges in MS 1900 implementation within Malaysia’s Public Higher Education Institution (MPHEI). A qualitative approach and case study strategy was used to explore the phenomenon of MS 1900 implementation in one of the MPHEIs. Semi-structured interview was employed as main data collection method, and it was triangulated with data collected from documents and observations. Interviewees that actively involved in MS 1900 implementation were selected from various categories which encompass lecturers, administrators, Shari’a officer, quality management officers and top management. NVIVO Version 10 was utilised to facilitate data analysis processes. The study found that there are challenges emerged from MS 1900 in MPHEIs namely employees attitude, some employees are reluctant to change conventional bank account to Islamic bank account, intense workload, too many responsibilities, lack of time, lack of training, lack of understanding towards MS 1900 and lack of manpower. This study adds to the knowledge of the emergence of the first ever Islamic QMS MS 1900. It also contributes a meticulous insights into the MS 1900 implementation within higher education environment, particularly in Malaysia. Remedial action should be taken to overcome all those challenges emerged so that MS 1900 implementation can be accomplished effectively. The findings from this paper can be employed by any university management or any organisation management as guideline in their attempt to implement QMS MS 1900 successfully.