Frederick II of Swabia was excommunicated and died in 1250. After him his son Manfredi, following what his father had said in his will, returned Putignano and the territories near the Abbey of Santo Stefano, there was no worse time than this for the territory and for the Putignanesi, in fact, the plague was added to the famine.
In 1317 Putignano and the monastery of Santo Stefano were declared Baliati and entrusted to the Knights of Malta with the title of Balì. The Knights of Malta who became Balì were holders of spiritual and temporal power. The Knights of Malta were friars soldiers obliged to take care of sick pilgrims and to defend Christianity from infidels with weapons.