The flag was altered as the nation changed from England to Great Britain to the United Kingdom.

Upon receiving a Royal Charter to trade in the Indian Ocean from Queen Elizabeth I in 1600, the English East India Company adopted a flag of red and white stripes (varying from nine to thirteen stripes in total), with the flag of England in the canton.

In Japan in 1616, the Company's ships were turned away because the cross on the flag was viewed as a symbol of Christianity, which the Japanese had banned in 1614.

[2][3] The Lê dynasty in Tonkin banned the Company from using the flag, believing the cross on it to be an endorsement of Christianity, promotion of which the Tonkinese had prohibited.

The Company then adopted a new flag including the King's Colours, as was shown when blue cloth, in addition to red and white, was requested for making a new flag for the fort in Bombay "if the King's colours were to be kept there; 'if not, white and red will be sufficient'".

"[9] This was a way of symbolising American loyalty to the Crown as well as the United States' aspirations, like those of the East India Company, to be self-governing.

Some colonists also felt that the Company could be a powerful ally in the American War of Independence, as they shared similar aims and grievances against Crown tax policies.