The Ottoman history of Sarajevo can easily be split into two halves. One is the city's golden age, the early Ottoman era, lasting from 1521 to 1697. The other is the late Ottoman era, from 1697 to 1878, which saw the decline of the empire, the city, and a number of disasters.

It is no coincidence that the beginning of the late Ottoman era in Sarajevo's history begins with the end of the Austro-Ottoman War. Following the failure at the Battle of Vienna in 1683, the western reaches of the empire were suspect to numerous raids. It was the raid of 1697 by Eugene of Savoy that would have the biggest impact. Brushing aside weak and unorganized defenses, Eugene was able to enter Sarajevo with ease. There, he pillaged the city like it had never been pillaged before, and once he was through with this he set the city to the torch.

Sarajevo was desolated by this attack. Very few structures survived the flames, and these were only ones built out of stone or subject to rare circumstance. The citizens of Sarajevo at that point had to start rebuilding their city from square one, not just structurally, but culturally and politically as well. By then, the seat of Bosnian government had already been transferred to Travnik, and the fire made the situation no better. For ten years between 1747 and 1757, the city even experienced anarchy.

If the city was no longer what it used to be structure wise, its intellectualism didn't suffer the slightest. In fact, the 18th century held many of Sarajevo's great thinkers, such as Mehmed Mejlija Guranij and Mula Mustafa Bašeskija. Significant libraries, schools, and mosques were built, as well as significant new fortifications.

The late 1700s however were not very good times. In 1788 another fire raged through Sarajevo, and this came only 5 years after an outbreak of plague. By the early 19th century, things did not get much better as Serbia gained its independence from the Ottoman Empire, creating a wedge between Sarajevo and Istanbul. This would all lead to the revolt of Bosniak national hero, Hussein Kapetan Gradašćević.

Demanding Bosnian independence from the Turks, Hussein Kapetan Gradašćević fought several battles around Bosnia. The last and ultimately most significant was the Battle of Sarajevo Field where Hussein Kapetan Gradašćević was betrayed by a fellow Bosniak and lost a hard fought battle. There he uttered his famous words "This is the last day of our freedom". For the next several decades no major developments occurred, as Sarajevo withered away in the sick man of Europe.