After the slavic invasions in the VI-VIII centuries, in 1040 it became the capital of the state of Zeta. With the fall of the power of the Nemanj in the century. XIV, Shkodra became part of the Balshaj principality who extended their possessions to Vlora. At the height of the rule and the greater extent of the possessions, the Balshays begin to face a new threat that is the Ottoman Turks. In April 1396, the city, together with the nearby castles of Drishti, Deja and Shas, as well as their territory, George II handed over to the Republic of Venice. In this period the Venetians rebuilt the castle and called the city Scutari. The city has institutions and laws like any developed Venetian center on the Adriatic.
In the spring of 1478 Sultan Mehmed II came by himself with large forces, but failed to conquer it and returned to Istanbul leaving a part of the army to continue the siege. The people of Shkodra and the Venetians persistently defended Shkodra, but finally, on January 25, 1479, they were forced to surrender after an agreement on fair terms. The war almost destroyed the city but it slowly recovered and in the 17th century became the center of the Ottoman Empire sanjak. In the early 18th century, 250 years of peace also brought economic prosperity. In this period the city has over 1,800 houses and has begun to extend to the area where it is today. Crafts, weapons, silk, copper and silver jewelry are developed there. From the middle of the century. XVIII Mehmet Pasha the Elder, of the Bushatli family, cunningly manages to be appointed ruler of the Sandzak. In 1757, he was given the title Pasha, thus paving the way for the rule of the Pashallek of Shkodra from the Bushatllinj dynasty. He established calm and order in the sanjak, and implemented the policy of religious tolerance, taking the clergy under his protection. He built bridges, roads and the first madrasa in Shkodra. In Shkodra there are still two buildings built to his order, the Middle Bridge and the Lead Mosque. In 1771 the High Gate gave him the rank of vizier and this date marks the creation of the Pashallëk of Shkodra, as a stable political territorial group that was governed autonomously, within the Ottoman state. After him, Mustafa Qorri took power, his rule did not last long as he soon died poisoned by the High Gate. A year before the death of his brother, the 20-year-old Mahmud Pasha, known in history as Kara Mahmud Pasha, or Mahmud Pasha the Black, had come to the throne of Shkodra. The young Pasha extended his rule to the vicinity of Ohrid and Korça. After several victories over the punitive Ottoman expeditions, Kara Mahmudi began to nurture the dream of an Albanian kingdom. In 1786, on his initiative, the leaders of the surrounding provinces gathered in Podgorica, where the establishment of the “Illyrian Confederation” was decided, which would fight for the achievement of full independence from the Ottoman Empire. In August 1787, the Turks again besieged Shkodra for 80 days, but thanks to secret cooperation with Ali Pasha Tepelena, the Turks withdrew. For not very clear reasons, Mahmud Pasha suddenly makes a strange move: he kills the Austrian envoys on the side of Lake Shkodra and again expresses loyalty to the Sultan. It was at this time that the sultan appointed him vizier. But that did not last long. In 1791 he helped the French monarchists, an action which irritated Sultan Selimi III, who again proclaimed Kara Mahmud “fermanli” (sentenced to death), but after international interventions, the Sultan forgave him and agreed to continue as vizier, but did not could cross the borders of the Shkodra sanjak. In 1796, he organized a major military campaign to extend the possessions in the direction of Montenegro. On September 22, 1796, the Albanians fell into the well and suffered defeat. Pashai was killed and beheaded. His brother, Ibrahim Pasha, took his place. He ruled until 1809. His story is that of a wise servant of Istanbul. Ibrahim Pasha is also known as the initiator of the construction of one of the most famous buildings of old Shkodra: Bexhistenit (closed bazaar), which was demolished by the communist government by blowing it up in 1969. The last ruler of the Bushatllinj dynasty was Mustafa Pasha. In 1830 he led the last Bushatllin uprising against the Ottomans. After being pardoned by the sultan he served for some time as a vali in Adana, Konya, Izmir and Bosnia. He died as the governor of Mecca, in 1860. In the nineteenth century, economic growth was rapid. The mall or bazaar has 2500-3500 shops. The city reaches 50,000 inhabitants and becomes the center of the Vilayet. Here are produced national clothing, fabric, leather, tobacco, gunpowder, caviar, which are exported. Oboti and Ulcinj were used as ports. In 1859-61 the Pontifical Seminary is established and the Franciscans establish their Assembly. In May 1862, Montenegrin forces launched attacks on the Highlands but were defeated by the Hoti and Gruda highlanders. One month later, numerous Montenegrin military forces attacked the island of Vranina. To protect the border point, which is on the northern side of Lake Shkodra, volunteers from the Shkodra youth came out, among whom was Oso Kuka. He was the commander of a small unit of about 20 men who defended Vranina Castle. Surrounded by a large number of Montenegrin soldiers, Oso Kuka blew up the tower with all his comrades, killing a large number of attackers and leaving the castle Albanian until 1879. In February 1867 the city became the center of the Archdiocese. There are commercial institutions of the time, court, postal directorate, customs. In 1865 the castle was abandoned after the Drin River changed its bed. Near the Bazaar there was a pier on the river Buna, where small boats and ships anchored between which Shkodra and its Bazaar were connected to the Adriatic. During the same period, literary, cultural and sports societies such as “Bashkimi” and “Agimi” were founded. On April 7, 1858, the construction of the Cathedral of Shkodra or the “Great Church” as it is called, one of the most beautiful Christian buildings in the Balkans begins. In April 1878, the League of Prizren was created for the non-partition of the lands of Albania and Shkodra became an important center of the national movement. The armies of Shkodra fight for the protection of the Albanian lands of Plava, Gucia, Hoti, Gruda, Ulcinj and Bar. In 1875, street lighting at night with kerosene lamps began by the Municipality of Shkodra. In 1878, the first music band of the country was established in Shkodra. The English Clock was built by the English Lord Padget at the end of the century. XIX. The city on June 1, 1905 experienced catastrophic events from the earthquake that caused great damage, killing 159 people and injuring 250 others. On April 6, 1911, the Albanian flag was raised in Bratile (Rudina), on the top of Deçiq. It was the first time that occurred after the fall of Shkodra in 1479. The uprising of 1911 in the northern area shook the Ottoman occupation in Albania.