Theoktistos in 842-843 made enough headway to install a Byzantine governor before having to abandon the campaign; the troops he left behind were quickly destroyed. The regent Bardas planned an expedition in 866 and was assassinated on the eve of departure. In 911, the admiral Himerios sailed with 177 ships and was defeated. In 949, Constantine Gongyles took 128 ships and suffered an even worse disaster. The pattern was always the same: the Byzantines could land on Crete, but Chandax sat behind walls strong enough to outlast any siege the supply lines from Constantinople could sustain. The Saracens waited the besiegers out, then attacked when hunger and disease had done their work.

Emperor Romanos II appointed Nikephoros Phokas, Domestic of the Schools of the East and a veteran of the wars against the Muslims in Asia Minor, to command the new expedition. Phokas mobilized the eastern army at a base south of Ephesus. The fleet that crossed the Aegean in autumn 960 included many dromons equipped with Greek fire. Using ramps, the troops disembarked in good order, formed up in three sections, and charged. The Saracen field army broke and fled into the fortifications. Phokas hoped to take Chandax by storm, but the walls held. He settled in for a long siege, building a fortified camp facing the city and ordering his fleet to blockade the harbor and intercept any vessel attempting to leave.

Phokas sent a senior officer, Nikephoros Pastilas, with a picked detachment to scout the interior and gather supplies. Pastilas found the countryside quiet and let his men relax. The Saracens, hidden in the heights, watched and waited. They attacked when the Byzantine soldiers were drunk and unprepared. Pastilas himself fell after multiple arrow wounds, and the column was cut to pieces. Almost no one survived to bring the news back. Phokas responded by leading a second night march, this time guided by local Christians, and surprising a 40,000-strong Saracen relief force in their camp. The relief army was annihilated. Phokas then ordered the heads of the fallen cut off; some were impaled within sight of Chandax's walls, others catapulted into the city. The defenders identified their kin among the heads and wept. They threw back his next assault anyway.

Phokas blockaded Chandax through the winter while his engineers built heavier siege machinery. Inside the city, food ran out. The Emir of Crete, Abd al-Aziz, sent envoys begging for aid. The Ikhshidid ruler of Egypt declined. The Fatimid caliph al-Mu'izz li-Din Allah saw an opportunity to claim leadership of jihad against Byzantium and promised to sail with his fleet on May 20, 961, from Tolmeita in Cyrenaica. He never got the chance. In March 961, Phokas launched the second assault. A battering ram pounded one section of wall to draw the defenders. While they concentrated there, Phokas's miners tunneled beneath another stretch of wall, packed the chamber with combustibles, and brought the whole section down. On March 6, the Byzantines poured through the breach. The defenders formed a line in the streets but could not hold. The traditional three days of plunder followed.

With Chandax fallen, the rest of Crete capitulated quickly. Byzantium reorganized the island as a regular theme governed from Chandax (the modern Heraklion), and saints like John Xenos and Nikon the Metanoeite led extensive missionary work to re-Christianize a population that had spent over 130 years under Muslim rule. The Aegean was, finally, Byzantine again. The cost showed up elsewhere. With so many troops committed to Crete and the eastern frontier, the Fatimids moved decisively against Byzantine Sicily, taking Taormina and besieging Rometta. When Phokas, by then emperor, sent a relief fleet in 964, it was destroyed at the Battle of the Straits. Sicily passed permanently into Muslim hands. In Crete itself, the memory of the siege survived for centuries; under later Venetian rule, Greek peasants still told stories about Phokas, and a much-distorted version of his governance entered local folklore. The walls of Chandax are mostly gone now, but the harbor where his fleet anchored is still in use.