Administration of Islamic matters in Malaysia is a subject that is usually misunderstood. The polemic on the status of Islam as the religion of the Federation but within the realm of power of the states creates confusion among those who are not familiar with the intricacies of the administrative aspect of Islamic matters in Malaysia. A study was conducted a decade ago to understand the relationship between Islam and federalism in Malaysia. One of the findings of this study is that administration of Islamic matters has progressed so much to the extent that, JAKIM, as the federal overseeing body, has established a number of cooperative federalism mechanisms to coordinate, consult and cooperate with the states without taking the states’ constitutional power in Islamic matters. The establishment of these cooperative federalism mechanisms was unplanned and unlabelled to the extent that it went unnoticed. This paper is an attempt to unravel the connection between administration of Islamic matters and cooperative federalism in Malaysia by focusing on the role of Department of Islamic Development Malaysia (JAKIM). This paper concludes that the ability of the Muslims in Malaysia and states to adopt and adapt with the religious regulations and restrictions during the Covid-19 pandemic is a culmination of a long-withstanding relationship, among others, cooperative federalism, between JAKIM and the states in the administration of Islamic matters in Malaysia.