In the 17th century, a Franciscan monastery was established in Valkininkai, becoming an important religious and cultural center in the region. With the founding of the monastery, a Jewish community also began to settle in the town — by 1642, they had received the privilege to operate a distillery.

In 1832, the monastery was closed by the Russian imperial authorities and converted into military barracks. By 1867–1868, the monastery buildings had been fully adapted for military use: the church towers were demolished, and part of the church was converted into an Orthodox church. The town and its surroundings lost a key landmark and cultural hub.

From 1920 to 1939, Valkininkai was under Polish occupation. Many residents emigrated, and the town's development stalled. The military continued to occupy the former monastery buildings. In 1939, Valkininkai was returned to Lithuania, but during World War II, the town suffered damage, and the former monastery was destroyed in an explosion.

Although the monastery buildings have not survived, the site itself remains a symbol of the region's religious heritageand the influence of the Franciscans on education and community life in Valkininkai.