In 1566 the castle of Gyula was occupied by the Ottoman army, and Békés fell under Ottoman rule too. The Ottomans built a motte castle in the town, but it was destroyed in 1595 when the Ottomans had to defend Gyula against the Hungarians who tried to get it back. The area became deserted. It was only exactly 100 years later, in 1695 that Békés was freed from Ottoman rule.
During the freedom fight led by Prince Francis II Rákóczi in the early 1700s the area of Békés was deserted again, for the last time. In 1720 John George Harruckern was granted Békés county via Royal Deed. He gave privileges to the serfs of the area, and gradually the population grew.
By the end of the 18th century the town already had its present five districts and the Protestant, Roman Catholic and Greek Orthodox churches and the Jewish Synagogue. The buildings of the Roman Catholic and Greek Orthodox churches and the Jewish Synagogue are all located within close proximity of each other. The annual floods of the Körös river meant a significant problem until the 1850s when the river was controlled.
In 1872 Békés was re-classified as a village. It was not until a hundred years later that it got its town status back.
Around the turn of the century Békés was rapidly developing and several new buildings were built. During the World Wars there were no significant battles in the area. Békés was freed from the Nazis on October 6, 1944. After the war industrialization quickened. On April 15, 1973 Békés was granted town status.
Before the 1944 Nazi deportation of Hungarian Jews to Auschwitz and other concentrations camps there were an estimated 600 members of the Synagogue in Békés; likely representing only a part of the greater Békés Jewish community. The first Synagogue in Békés was built in 1660 CE (during the Ottoman period in Békés), constructed of wood, but later burned down in a fire. During the Ottoman period, many Sephardic Jews fleeing Spain in the post-1492 Spanish Inquisition and Expulsion period immigrated to locations within the Ottoman Empire, which granted citizenship and tolerance to Jews. This may also be the origin of the first Jewish community in Békés.
In 1905, the current Synagogue was constructed with traditional stone construction techniques.
After 1945, the Synagogue, in its destroyed condition, was used as storage facilities for local craftsman. At some time after this, KISZ - the Communist Youth Association - renovated the building and used it as their club house. Today, the Synagogue houses the non-profit organization, Mégis Van Remény Egyesület (lit. 'There Still is Hope Association'), that runs a community center and restaurant in the building. 'Mégis Van Remény' hopes one day to find the funding to restore the Judaica of the original Synagogue as a memorial of the Holocaust and the Békés Jewish community that perished in the Shoah.
Today, Békés is made of several ethnic groups, including Hungarians, Roma, and with its near proximity to the Romanian border, Romanians who constitute approximately 5% of the population.