Muslims have unique characters which are closely related to their religious background. With the high growth of e-commerce in Indonesia, it is important to study Muslim market segments where Indonesia itself is a country with the largest Muslim population in the World. The progress of the halal financial industry and business also triggers the e-commerce development among Muslim Millennials. Muslim Millennials will become the main market and the largest customer segment In Indonesia since one-third of its population is dominated by millennials. The aim of this research is to develop and test a comprehensive model that explains how Muslim Millennials develop loyalty to online shopping websites (e-commerce). To test the research model, the online survey was distributed to a random sample of highly educated Muslim Millennials. The results found that positive online experience (flow) is the most important antecedent of e-loyalty in e-commerce websites for Muslim Millennials. Brand equity is also a key precursor of e-loyalty. However, trust is not a significant precursor of e-loyalty for Muslim Millennials in Indonesia.