The Khojas are a caste-based community that emerged in the fourteenth century across Sindh, Kutch, and Kathiawar.* For centuries, they maintained a distinct identity that blended Hindu and Islamic traditions, which resisted rigid classification within either religious framework. The nineteenth century, however, brought profound change through two major schisms that reshaped their religious and social identity. The first, rooted in disputes over the authority of the Aga Khan, culminated in the 1866 Aga Khan Case and prompted some to align with Sunni Islam. The second, a theological rupture, led to the rise of Isna Ashari Khojas. This shift was influenced by Twelver Shiʿi mujtahids in Najaf and Karbala, who, through Indian Shiʿi ʿulamāʾ and mullās, reshaped Khoja religious identity. This article explores the central role of Twelver Shiʿi networks and their transregional reach in shaping this transformation. It focuses on how changes in legal identity, religious authority, and migratory patterns across Bombay, Zanzibar, and the shrine cities of Iraq contributed to the emergence of a distinct Isna Ashari Khoja identity. In doing so, it situates Khoja transformations within a wider historical context of religious affiliation and social organisation across South Asia and East Africa.