In 1260, Michael began the assault on Constantinople itself, which his predecessors had been unable to do. He allied with Genoa, and his general Alexios Strategopoulos spent months observing Constantinople in order to plan his attack. In July 1261, as most of the Latin army was fighting elsewhere, Alexius was able to convince the guards to open the gates of the city. Once inside he burned the Venetian quarter (as Venice was an enemy of Genoa, and had been largely responsible for the capture of the city in 1204).

Michael was recognized as emperor a few weeks later, restoring the Byzantine Empire under the Palaiologos dynasty, after an interval of 57 years where the city had been the capital of the Latin Empire installed by the Fourth Crusade in 1204. Achaea was soon recaptured, but Trebizond and Epirus remained independent Byzantine Greek states. The restored empire also faced a new threat from the Ottomans, when they arose to replace the Seljuks.