Qabatiya, like all of Palestine was incorporated into the Ottoman Empire in 1517. In the 1596 tax registers, it was part of the nahiya of Jabal Sami, part of the larger Sanjak of Nablus. It had a population of 89 households and 18 bachelors, all Muslims. The inhabitants paid a fixed tax rate of 33.3% on agricultural products, including wheat, barley, summer crops, olive trees, goats and beehives, in addition to occasional revenues; a total of 14,920 akçe. Half of the revenues went to the Tarabay Bey of Lajjun. In 1105 AH Abd al-Ghani al-Nabulsi mentioned a village on the road from Nablus to Jenin. in 1838 Edward Robinson found it to be a very large village, surrounded by very extensive and beautiful olive groves, while in 1850, it was described as surrounded by gardens, built on the side of a wooden hill, covered with olive trees. In 1870 Victor Guérin found gardens around Koubatieh planted with fig, olive and pomegranate trees, with vegetables underneath. It was a large village, divided into several areas under the jurisdiction of many different sheikhs. He further noted that “Kubataieh stands upon a rocky hill, whose sides are pierced by numerous cisterns of ancient origin, some of which are partly filled up and in bad repair ; others are still used by the people. The latter are closed at the mouth by great round stones in form of a mill-stone, pierced in the centre. This second opening is itself closed by another stone, which is taken away when the water is drawn. This system of closed wells and cisterns by means of a stone is of extreme antiquity.” In 1882, the PEF's Survey of Western Palestine described it as a “large stone village on a slope, east of a small plain which is full of olives. It has a sacred place on the south, and a good orange garden near the village.”
In the 1922 census of Palestine, conducted by the British Mandate authorities, Qabatiya had 1,803 inhabitants; 1,799 Muslims and 4 Christians, where the Christians were all Orthodox. This increased to 2,447 in the 1931 census; 2 Christians and the rest Muslims, in a total of 551 houses. In the 1945 statistics the population of Qabatiya, together with Kh. Tannin, was 3,670, all Muslims, with 50,547 dunams of land, according to an official land and population survey. 9,542 dunams were used for plantations and irrigable land, 21,464 dunams for cereals, while 113 dunams were built-up land and 19,428 sunams were classified as "non-cultivable".
Since the Six-Day War in 1967, Qabatiya has been under Israeli occupation. After Oslo II in 1995, Qabatiya came under Palestinian Authority administration, in what is now known as Areas A and B. Approximately ten Palestinians were killed between October 2015 and July 2016 while carrying out attacks against Israelis. In July 2016, clashes between Palestinians and Israeli armed forces occurred during a house demolition by Israel of a man accused of being involved in an attack in Jerusalem. The Israeli military reported that the military convoy that carried out the demolition was met by Molotov cocktails and fire from improvised guns. Palestinian officials reported six Palestinians wounded in the exchange, with the Israeli military confirming three Palestinians hit. Israel calls the demolition of homes of attackers as a deterrent to violence, while human rights groups and Palestinians condemn it as a form of collective punishment.
