[6]: 257 During this period, the sanjak of Rakka was "fully integrated into the empire's military-administrative structure", with Ottoman officials directly in charge.

[6]: 256  The kadı, in additional to his judicial role, was responsible for collecting waqf dues from nomadic tribes, report and address abuses by tax farmers, and act as a check on the sanjak-bey's power.

[6]: 257 In the late 1500s, the Ottoman administrative system was shifting away from military-command-based sanjaks as the basic territorial unity of the empire and replacing them with taxation-based eyalets.

[6]: 258  This trend, as well as an "increasing awareness of the Middle Euphrates's productive capacity", a need for the Ottomans to secure the frontier, and the temporary importance of the region due to the war with the Safavids from 1578 to 1590, all factored into the creation of the Eyalet of Rakka in 1586.

[6]: 258–9 The Celali rebellions and the costly Ottoman–Habsburg wars caused Ottoman central authority to decline in Rakka Eyalet in the early 1600s.

[6]: 260  The citadel in Raqqa was renovated in 1683, and then the iskan program began in earnest under Kadızade Hüseyin Paşa, who was the eyalet's governor from 1590 to 1595.

[6]: 261  Hüseyin was tasked with settling Turkmen and Kurdish tribes from Anatolia in the eyalet, particularly in the Balikh valley upstream from Raqqa.