The church that traced its foundation back to Thomas was united until a revolt against the Portuguese missionaries in the 17th century. According to church historians, the church founded by Thomas developed a distinct identity over the centuries, assimilating Hindu traditions and practices into Christian and church life while following Oriental worship, under the jurisdiction of Persian bishops. Thus, church feasts and fasts, marriage ceremonies, rites associated with birth and death, the training of clergy and the administration of the churches all became influenced by Hindu customs. Similarly, Hindu fertility rites take place during the reception after the church marriage ceremony. In a land where kneeling is not the general practice for worship, St. Thomas Christians prefer sitting, squatting or standing.
Indian influence is evident in the given names of church members.
When the Portuguese established themselves in India in the 16th century, they found the church in Kerala as an administratively independent entity. By the end of the century, the St. Thomas Christians had been brought under Catholic rule. The local Christians who remained loyal to Rome eventually became known as the Syro Malabar church. Those who had risen in revolt in 1653 came into contact with the Patriarch of Antioch, becoming known as Jacobites or Orthodox Christians. However, with the passage of time, the Orthodox community underwent further divisions.