Baybars, one of the great Ayyubid commanders, seized power in the aftermath of Shajarat Ad-Durr's murder but his heirs were murdered by Qalawun, another Mamluke who established the Bahri Mamluke dynasty, named after the Mamluke garrison along the Nile River (Bahr Al-Nil).

During his reign Sultan Qalawun became a great patron of architecture and constructed mosques, fortresses and other buildings in Cairo. Qalawun also established relations many foreign countries in Europe, Africa and Asia. Qalawun's son and successor, Mohammed An-Nasir who reigned for nearly half a century, from 1294-1340, was also a great patron of architecture.

The Mamluke armies of Sultan Mohammed An-Nasir shocked the seemingly unstoppable Mongol armies by defeating them on the Syrian battlefield. The descendants of Mohammed An-Nasir were weak and the Turkish Bahri Mamluke dynasty gradually lost control of the sultanate which was seized by the Circassian Mamluke Barquq who established the Burgi Mamluke dynasty, named after the Mamluke garrison set beneath the Citadel In Cairo. Although Sultan Mohammed An-Nasir had made a treaty with the Mongols, they remained on the borders of Syria and Sultan Barquq campaigned against the Mongols to drive them out of the Near East altogether.

Heavy taxation was levied to pay for these campaigns, debilitating the economy of Egypt. Conditions were exacerbated by a plague that swept through the country during the reign of Barquq's son Farag. It was not until the reign of Sultan Barsbey that Egypt regain its power. Barsbey recognized the rising power and potential threat of the Ottoman Turks and established good relations with them. He also extended Mamluki trade. Nevertheless, the Mamluke economy remained unstable for nearly a century until the reign of Sultan Qait Bey, another great Mamluki builder, who constructed mosques, madrassas and other buildings throughout the empire.

The 46th Mamluki sultan was Qansuh Al Ghuri who continued the Mamluki architectural tradition but saw his economy crash after European traders began using the Cape of Good Hope for their spice trade rather than trading through Cairo. To add insult to injury, the Ottomans attacked Mamluke Syria and Sultan Qansuh fell in battle in 1516. The following year Tuman was executed by the Ottomans, signaling the end of the Mamluke Empire and the beginning of Ottoman rule, but the Mamlukes remained a powerful force within Egypt throughout the Ottoman period and beyond.