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In 1534, Jokūbas Astikas gifted Alanta church with Dapkūniškiai farmstead, including its inn, tithe from Alanta (Naujasodis) estate and other lands. In 1575, Jurgis Astikas provided the church with new lands instead of the tithe. All the priests in Alanta died during the plague in 1656 and all church related matters were assumed by the manor estate. The high altar was taken to Kavarskas church, and a new priest was once again appointed in 1658.
In 1675, the church was of cross-plan, without any towers, with two side chapels, one of which was restored while the other old one was abandoned. The church was temporarily covered with straw. In 1682, Džiugai and Luciūnai villages were gifted to the clergy house. The parsonage owned Duobiniai and Kazlai villages in 1818. The church was extended and its altars were re-positioned in 1827 under the care of pastor Antanas Mažeika.
In 1903, the project of a new brick church was prepared by Swedish architect Karl Eduard Strandmann which was worth 37 396 roubles. From 1904 to 1909, the church was bricked, its presbytery was plastered, the altar of the old church was placed and church services were once again held. Constructions of the church were fully completed in 1912 under the care of pastor Domininkas Vainauskis. The church was equipped after World War I.
In 1915, the Germans took the metal parts of the organ. In 1921, the church was consecrated by bishop Pranciškus Karevičius. Altars of the church were re-positioned in 1929–1931. In 1937, artists Benediktas Zakarka and Pranas Zakarka renewed and repainted the interior of the church and made paintings for the chapel under the care of pastor Adomas Vyšniauskas. The towers and walls of the church were damaged in 1944. Later, the church was repaired. Pastor Konstantinas Šimašis (1888–1955) was arrested in 1951 and sentenced to 10 years in prison.
The pastor of Alanta Sigitas Sudentas was the confessor of president A. Brazauskas.
The church is of neo-Romanticism style, with a Latin cross plan, hall space, with a half-circle apse and two 51 m high facade towers. Its interior is comprised of three naves. The fence of the churchyard is masonry.