In August 1869, a large force led by Nasir bin Mubarak invaded Bahrain and killed Isa's father, Sheikh Ali.

Sheikh Isa fled to Zubarah, to be treated by the Al Noaim tribe who remained loyal to his rule.

The protectorate treaty was confirmed and extended on 13 March 1892, in which Isa also reiterating his desire to retain for himself the right to manage Bahrain's internal affairs.

[2] From 1926, at an old age, Isa was joined by a British consultant, Charles Belgrave, who helped him implement administrative reforms aimed at promoting social progress as laws for the regulation of pearl fishing, traditionally one of the main parts of the local economy.

Sheikh Isa died while praying the dawn prayers in his room in Muharraq on 9 December 1932 after a reign of 63 years, and was buried at Al Muharaq cemetery.