On arriving in Bombay, the British made a fresh effort to win permission for his return to Iran, while the Aga Khan had also written a letter about it to the new Iranian king, Nasiruddin Shah's chief minister, Amir Kabir, who proved less responsive than his predecessor, insisting that the Aga Khan would be arrested at the borders as a fugitive. After the execution of Amir Kabir in 1268/1852, the Aga Khan made a final plea to return to his homeland, and sent Nasiruddin Shah an elephant and a giraffe as gifts. He also sent gifts to Amir Kabir's successor, Mirza Aqa Khan Nuri, who was a personal friend of the Aga Khan. Some of the Aga Khan's family estates in Iran were then restored to the control of his relative, but the new minister was unable to arrange for his return. Meanwhile, the Bombay Government approached the Aga Khan to get a definite answer regarding his stay. On September, 1850, the deputy Secretary in the Iranian Department of Bombay personally asked the Aga Khan, who stated that he was willing to stay in Bombay. The members of the India Board also approved it on January 22, 1851. In April 17, 1851, the Bombay Government apprized the Aga Khan of the decision of the court directors. The Aga Khan on April 18, 1851 wrote a letter to Bombay Government, expressing his gratitude.
In India, the Aga Khan retained his close relation with the British empire. On a rare occasion, the Aga Khan was visited in his Bombay home, the Aga Hall, by the Duke of Edinburgh, the future king Edward VII (1901-1910), as Prince of Wales, during a state visit to India, and held a long talk with him. The two sat in front of a portrait of Shah Fateh Ali, the emperor of Iran, whose daughter the Aga Khan had married. The Prince of Wales inspected the Aga Khan's cups won on the Indian turf and his son's trophies of the Indian chase, and talked over some of the events of a life as varied and adventurous as that of the Aga Khan's ancestor, who seven centuries ago wrote to Leopold, Duke of Austria, urging the release of Richard Coeur de Lion, then a prisoner in the hands of Leopold at the time of the Crusades. In sum, it was an honour which, with the exception of the leading ruling princes, was accorded to no other nobleman and was acknowledged of his princely birth and the admirable services he had rendered to the British government. Writing on the historic visit, Sir Bartle Frere said, "There can be little doubt that the visit has been described and discussed in many a meeting of the Aga Khan's followers in India, Persia and Arabia - on the remote shores of Eastern Africa, and in still more inaccessible valleys of Central Asia, and it will doubtless find a place in the annals of this singular sect for many centuries to come."
The Aga Khan thus received government protection in British India as the spiritual head of the Shia Ismaili Muslims, which solidified his position and helped him in the exercise of his authority. During three decades of residency in Bombay, he exerted a great deal of direct control over the Ismaili community, and organised the community more progressive under the network of leaders and officers.
Kutchh in the meantime, reported to have gripped in a dust bowl, followed by a terrible famine, and as a result, a retinue of ten thousand Ismailis tracked down in Sind. On the instructions of Governor General, Sir Charles Napier granted them permission to settle down at Mullah Khatiar (Matli), and most of the Ismailis also migrated to Karachi.