Since the take of Fort Jesus in December 1698, the sultanate of Oman started governing from Muscat over the formerly wealthy cities of the Swahili coast, north of Cape Delgado (Mozambique). However, the ports of East Africa failed to recover the splendour they achieved in the past, since the new metropolis exerted identical control on traffic along the Indian Ocean commercial routes. This, together with the tyranny of the Omani governors in the coastal cities, drove an uprising against the invaders in Mombasa and Pate, where the Imperial representatives were murdered and the citizens refused to pay the sultanate's taxes. Hence started a period of small wars between the cities still under the control of Oman and those in which the rebels had seized power and declared independence.

An attempt to solve the revolts was to hand out the ruling of the cities to Swahili families which remained loyal to Muscat. In Mombasa, the Mazrui dynasty was appointed to govern the island in 1741. However, the operation was not successful as expected: after the murder of the sultan of Oman, Saif ib Sultan, the first Mazrui governor of Mombasa, Muhammad ibn Uthman al-Mazrui, refused to subordinate to the new ruler, Said al-Busaidi. The new sultan, resolved to terminate the insurrection in Mombasa, commissioned a fleet to murder al-Mazrui and take Fort Jesus. But one year later, one of al-Mazrui's brothers murdered the new governor and retrieved the Fort. The effect of rebelion spread to other coastal cities and the isle of Pemba.

Internal clashes in the ruling dynasty in Muscat also affected the stability of the East African coast. In 1784, a brother of sultan Busaidi seized the south strip of the shoreline, taking Kilwa and Zanzibar with the aim of creating his own sultanate. The sultan reacted rapidly and retrieved the possessions of his rebel brother, an operation that allowed him to retrieve as well the rest of the revolted cities.

Thus started a brief peaceful period under the central Muscat government, until in the early 19th century the Mazruis stroke back. They launched a campaign to seize the coastal cities, from Pangani to Malindi. At the same time a new powerful sultan was taking over the Crown in Oman, after murdering his brother in 1806: Seyyid Said. Meanwhile, the two emerging imperial powers, England and France, were contending on the trading routes with India. France dominated over the Isle of France, Bourbon, Seychelles and the Isle of Rodriguez. In order to supply slaves to the sugarcane plantations at their Indic colonies, the French controlled the slave trade at the south coast, with Kilwa, in Oman's hands, as their main supply center. The defeat of Napoleon in 1815 allowed the English to expand their power to Seychelles and Isle of France. Seyyid Said's father had signed an alliance with the victors, of which the sultan took advantage to request their help in an operation to re-conquer the East African coast.

An important conflict was clouding the alliance between Oman and England: the British wished to abolish the slave trade, the main source of wealth for the sultanate. The Omanis had flourishing slave trade centers in Kilwa, Bagamayo and zanzibar, the latter to supply India and the Arab countries. Besides, the growing power of the British Empire made clear who ruled now in the Indic scenario. Reluctantly, in 1822 the sultan was bound by the governor of Mauritius to sign a treaty abolishing the human trade. Actually, this agreement had political intentions: it did not affect traffic with the Arab countries, but it was good to cut off the supply of slaves from the Omani possessions to the French colonies.

The Mazruis would not remain silent for long. In view of their expansionist ambitions, other coastal ports felt themselves threatened. In 1822, the Pate governors requested help from the sultan, who sent his troops against Mombasa. On the other hand, the sympathy of the British, the new rulers of the Indian Ocean, was on dispute. The Mazruis had already applied for their favours, being rejected twice by virtue of the Anglo-Omani alliance. But in 1824 captain Owen, in command of the ship HMS Leven, docked at the Mombasa Port right at the time when the sultan's navy was assaulting Fort Jesus. In an unilateral decision, Owen resolved to support the Mazruis, feeling that the establishment of a British base in Mombasa could firmly promote abolition of the slave trade in the region. A 21-year old Lieutenant Reitz disembarked with a small contingent and set the British flag in Mombasa, declaring the first English protectorate. Later on, in 1826, the sultan's pressures obliged England to abjure.

The vain first attempt of the sultan to retrieve Mombasa was followed by a second one, until finally Said's son conquered the city for his father. In 1840, the whole coast was finally in the sultan's hands. Understanding that the region needed a closer control, the same year Seyyid Said decided to move the Oman sultanate's capital from Muscat to Zanzibar. The resolution was also economy-driven: besides ivory, beeswax and tortoise shells, the traditional commerce in the island, it was emerging as a high ranking slave trade center. Said left his son Seyyid Thuwani in Muscat to take over the Oman's affairs.

The island met a new splendour period on behalf of its new status. The sultan expanded the clove plantations and extended them to the isle of Pemba, dominating four fifths of the world production. After slaves and ivory, clove became the third source of exports. On political grounds, Said finally defeated the Mazruis, whose major leaders had been arrested and deported in 1837.

The flourishing development of the Zanzibar sultanate firmly contributed to increase the Europeans' interest in dominating East Africa. Commercial relationships with the foreign powers led to the establishment of consulates by England, Germany, Portugal, United States and France. To avoid excessive dependence on the English, the sultan signed trade agreements with France and Germany, improving his contacts with America. However, his tendency towards the British obliged him in 1845 to sign a new treaty with the English consul Hamerton for banning slave exports. Once more and in spite of the agreement, the trade went on.

In 1856, Said died from dysentery. His son Seyyid Majid, with the support of slave traders and the British, proclaimed himself the new sultan of Zanzibar and the East African coast. This move was not accepted by his brother Thuwani in Oman, who considered himself the legitimate heir. The conflict was solved with a split off, guaranteed by Britain: Thuwani retained Oman, while Majid was taking over Zanzibar and the coast. In that way, East Africa was definitely torn off Oman sultanate.