The Ottomans reorganised the Bulgarian territories as the Beyerlik of Rumili, ruled by a Beylerbey at Sofia. This territory, which included Thrace and Macedonia, was divided into five sanjaks, each ruled by a Sanjakbey accountable to the Beylerbey. The Ottoman Empire existed primarily to fight wars. Once an area was conquered, the Ottomans lost interest in it. They called their non-Muslim subjects rayah - cattle, which suggested an attitude of benign indifference. The conquered land was parcelled out to the Sultan's followers, who held it as feudal fiefs (timars and ziamets) directly from him. The land could not be sold or inherited, but reverted to the Sultan when the fiefholder died. So long as this system applied, the Bulgarian peasants were in some ways better off than they had been under the rule of the boyars.

The Ottomans did not require the Bulgarians to become Muslims, although many did so. Provided they paid their taxes and gave no trouble, they were left to themselves. Non-Muslims did not serve in the Sultan's army, so the burden of conscription was lifted from the peasants. The exception to this was the "tribute of children," whereby every Christian community was required to give one son in five to be raised as a Muslim and enrolled in the corps of Janissaries (yenicheri or "new force"), an elite unit of the Ottoman army. The Bulgarians also paid a capitation tax and a levy on commerce, but these were collected irregularly by the inefficient Ottoman administration.

The Sultan regarded the Ecumenical Patriarch of the Greek Orthodox Church as the leader of the Christian peoples of his empire. The independent Bulgarian Patriachate was suppressed, and the Greek Patriarch given control of the Bulgarian Church. This remained a source of discontent throughout the Ottoman period. Although Bulgaria was better governed than some parts of the Balkans because it was closer to Constantinople, economic activity and population declined through neglect and restrictions on movement. Large numbers of Turks settled in Bulgaria, particularly in the south-east around Kurdzhali and in the north-east around Shumen. Since few outside the church were literate, the dominance of the Greek clergy led to the near-extinction of Bulgarian culture. There was not a single Bulgarian-language school in the country until 1835.

Nevertheless, while the Ottomans were ascendant, there was little overt opposition to their rule. In 1595 and 1688 the Austrians incited rebellions in Bulgaria as part of their long war with the Ottomans, but these were easily suppressed. In 1739 the Peace of Belgrade between Austria and the Ottoman Empire ended Austrian interest in the Balkans for a century. But by the 18th century the rising power of Russia was making itself felt in the area. The Russians, as fellow Orthodox Slavs, could appeal to the Bulgarians in a way that the Austrians could not. The Treaty of Kuchuk-Kainarji of 1774 gave Russia the right to interfere in Ottoman affairs to protect the Sultan's Christian subjects. Ironically, this led the Ottomans to see the Bulgarians as potential enemies and made their situation worse.