Shajar al-Durr became a central figure during the final Ayyubid crisis. When al-Salih died in November 1249 during Louis IX's invasion of Egypt, she concealed the sultan's death from the army. She maintained the appearance of continuity in command while summoning the crown prince, Turan-Shah, from Mesopotamia.

Her actions helped preserve Egyptian military cohesion during the campaign. At Mansura in February 1250, the Kurdish and Arab troops fled, but the disciplined Turkish mamluks defended the Ayyubid position. Their later victory at al-Fariskur led to the capture of Louis IX and the collapse of the immediate Crusader threat.

After Turan-Shah became unpopular with the leading mamluk officers, a group led by Baybars murdered him in May 1250. The officers then proclaimed Shajar al-Durr sultan of Egypt and queen of the Muslims, an unusual instance of a woman formally attaining sovereign status in Islamic lands. After eighty days of solitary rule, she married Aybeg, who became the first Mamluk sultan.