Bosnia was rapidly absorbed into the Ottoman Empire and was divided into military-administrative districts, or sanjaks (from the Turkish sancàk, meaning “banner”). In 1580 a broad area covering modern Bosnia and some surrounding areas of Croatia and Serbia was given the full status of an eyalet, or constituent province of the empire. Bosnia enjoyed this status as a distinct entity throughout the rest of the Ottoman period. The Bosnian eyalet was governed by a vizier and administered through a network of junior pashas and local judges. Land was distributed according to the Ottoman feudal system, in which the holder of a timar (estate) had to report for military duty, bringing and supporting other soldiers. A wide range of taxes was imposed, including the harač, a graduated poll tax on non-Muslims. Also introduced was the notorious system called devşirme, under which Christian boys aged 10 and above were taken off for training in the imperial administration and the Janissary corps, an elite army division. In all these respects, conditions in Bosnia were similar to those in the other conquered areas of Europe.

In one crucial way, however, Bosnia differed from the other Balkan lands (except, later, Albania): a large part of the native population converted to Islam. This was a gradual development; it took more than a hundred years for Muslims to become an absolute majority. There was no mass conversion at the outset, nor mass immigration of Muslims from Anatolia. The fundamental reason for the growth of such a large Muslim population in Bosnia may lie in the earlier religious history of the Bosnian state. Whereas neighbouring Serbia had benefited from a strong, territorially organized national church, Bosnia had seen competition in most areas between the Bosnian church and the Roman Catholic Church, both of which operated only out of monastic houses. In Herzegovina a third church, the Serbian Orthodox, had competed. Christianity was thus structurally weaker in Bosnia than in almost any other part of the Balkans. The motives that inclined Bosnians to adopt Islam were partly economic: the prosperous cities of Sarajevo and Mostar were also mainly Muslim, and it was not possible to lead a full civic life there without converting to Islam. Other motives included the privileged legal status enjoyed by Muslims and, possibly, a desire to avoid the poll tax on non-Muslims, though Muslims were subject, unlike Christians, both to the alms tax and to the duties of general military service. But the traditional belief that Bosnian noblemen converted en masse to Islam in order to keep their estates has been largely disproved by modern historians.

Another way in which Bosnia differed from other parts of the Ottoman Balkans is that, for most of the Ottoman period, Bosnia was a frontier province, facing some of the empire’s most important enemies— Austria, Hungary, and Venice. To fill up depopulated areas of northern and western Bosnia, the Ottomans encouraged the migration of large numbers of hardy settlers with military skills from Serbia and Herzegovina. Some of these settlers were Vlachs, members of a pre-Slav Balkan population that had acquired a Latinate language and specialized in stock breeding, horse raising, long-distance trade, and fighting. Most were members of the Serbian Orthodox Church. Before the Ottoman conquest, that church had had very few members in the Bosnian lands outside Herzegovina and the eastern strip of the Drina valley. There is no definite evidence of any Orthodox church buildings in central, northern, or western Bosnia before 1463. During the 16th century, however, several Orthodox monasteries were built in those parts of Bosnia, apparently to serve the newly settled Orthodox population there.

Major wars affecting Bosnia took place almost every two generations throughout the Ottoman period. Bosnia was an important recruiting ground for Süleyman I’s campaign to conquer Hungary (1520–33). There was fighting on Bosnia’s borders during his final Hungarian campaign of 1566. And the large-scale Habsburg-Ottoman conflict of 1593–1606 was sparked by fighting in the Bihać region of northwestern Bosnia. This war left Bosnia financially drained and militarily exhausted. A Venetian-Ottoman war, beginning in the 1640s and lasting until 1669, involved heavy fighting and destruction in parts of western Bosnia. In the Habsburg-Ottoman war of 1683–99, Austria reconquered Ottoman Hungary and Slavonia, sending a flood of Muslim refugees (mainly converted Slavs) into Bosnia. In 1697 a small Austrian army under Prince Eugene of Savoy marched into the heart of Bosnia, put Sarajevo to the torch, and hurried back to Austrian territory, taking thousands of Roman Catholic Bosnians with it. In the next major war (1714–18), Austria joined forces with Venice, and in the Treaty of Passarowitz (Požarevac, Serbia) in 1718, Venetian-ruled Dalmatia was allowed to extend its territory inland, reaching a line that since then has formed part of the southwestern border of Bosnia. Austria invaded Bosnia again in 1736 but was repelled by local forces. In the subsequent peace settlement (the Treaty of Belgrade, 1739), Austria gave up its claim to the territory south of the Sava River. This settlement formed the basis of the northern border of modern Bosnia. Austria seized more territory after invading Bosnia again in 1788, but it yielded up its gains at the peace settlement in 1791.

The chronic fighting weakened Bosnia. War necessitated increased taxation, causing tax revolts. Forced conscription and frequent plague epidemics led to a relative reduction in the Muslim population, which contributed its manpower to Ottoman campaigns throughout the empire and may have suffered disproportionately from the effects of plague in the cities. In the 18th century there was strong growth in the Christian population; by the end of the century the Muslims were probably no longer in the majority. The social consequences of war also included a change in the system of land tenure: increasingly, the old feudal timar estates were converted into a type of private estate known as a çiftlik, in response to the imperial treasury’s need for cash instead of old-style feudal service. The conditions of work demanded of the peasants on these estates were usually much more severe, and these peasants tended increasingly to be Christians, since Muslim peasants were able to acquire smallholdings in their own right.

Nevertheless, Ottoman Bosnia was not permanently sunk in misery. Descriptions of Sarajevo by visiting travelers portray it as one of the wonders of the Balkans, with fountains, bridges, schools, libraries, and mosques. Fine mosques were also built in towns such as Foča and Banja Luka. (Many of these buildings were systematically demolished by Serb forces in 1992–93.) Numerous works of poetry, philosophy, and theology were written. The cities of Sarajevo and Mostar, where such urban culture flourished, enjoyed a large degree of autonomy under elected officials. After war forced the Bosnian viziers to move out of Sarajevo in the 1690s, they found it almost impossible to return, residing instead in the town of Travnik and exercising only limited power. Real local power passed increasingly into the hands of a type of hereditary official (unique to the Bosnian eyalet) known as a kapetan.

The existence of these powerful local institutions meant that Bosnia was well equipped to resist the reforming measures that the Ottoman sultans began to issue in the early 19th century. When Sultan Mahmud II reformed the military in 1826 and abolished the Janissary corps (which had acquired the status of a privileged social institution), the reform was fiercely resisted by local Janissaries in Bosnia. The Ottoman authorities mounted punitive campaigns against the Janissaries’ stronghold, Sarajevo, in 1827 and 1828. In 1831 a charismatic young kapetan called Husein seized power in Bosnia, imprisoning the vizier in Travnik. With an army of 25,000 men, Husein then marched into Kosovo to negotiate with the Ottoman grand vizier, demanding local autonomy for Bosnia and an end to the reform process there. But the grand vizier stirred up a rivalry between Husein and the leading kapetan of Herzegovina, Ali-aga Rizvanbegović, and in the following year Husein’s support melted away when a large Ottoman army entered Bosnia. Rizvanbegović’s reward was that Herzegovina was separated from the Bosnian eyalet as a distinct territory under his rule. Further reforms announced by Sultan Abdülmecid I, involving new rights for Christian subjects, a new basis for army conscription, and an end to the much-hated system of tax-farming, were either resisted or ignored by the powerful Bosnian landowners.

During these final decades of Ottoman rule, the rise of Serbia as a quasi-autonomous Christian province, from which Muslims were violently expelled, made Bosnian Muslims feel more isolated and vulnerable. The increasing role of foreign powers (especially Austria and Russia) as “protectors” of the interests of Christians in the Balkans also raised Bosnian suspicions. Bosnian landowners, feeling that they could no longer trust the Ottoman authorities in Constantinople (now Istanbul) to maintain their power, frequently turned to more repressive measures against their Christian subjects.

However, two Bosnian governors succeeded in forcing through some of the sultan’s reforms and curbing local resistance. The first of these, Omer-paša Latas, crushed a major rebellion in 1850–51 and revoked the separate status of Herzegovina. The second, Topal Osman-paša, introduced a new method of military conscription in 1865 and a completely new administrative system in 1866, dividing Bosnia into seven sanjaks and establishing a consultative assembly. He also built schools, roads, and a public hospital and allowed the two Christian communities to build new schools and churches of their own. Yet the growing tax demands on Bosnian peasants revived local resistance.

In 1875 a revolt against the state tax collectors began among Christian peasants in the Nevesinje region of Herzegovina. Unrest soon spread to other areas of Bosnia, and repressive force was applied both by the new Bosnian governor and by local landowners using their own irregular troops. The revolt aroused enormous popular sympathy in Serbia, which, along with Montenegro, declared war on the Ottoman Empire in 1876. Russia came into the war on their behalf in the following year. After the Serbo-Turkish War ended in 1878, the other great powers of Europe intervened at the Congress of Berlin to counterbalance Russia’s new influence in the Balkans. The congress decided that Bosnia and Herzegovina, while remaining notionally under Turkish sovereignty, would be occupied and governed by Austria-Hungary. In 1878 Austro-Hungarian troops took control of Bosnia, overcoming vigorous resistance from local Bosnian forces. They also occupied the neighbouring sanjak of Novi Pazar (now in Serbia), which had been one of the seven Bosnian sanjaks in the late Ottoman period.