Baclayon church was declared a National Cultural Treasure by the National Museum of the Philippines and a National Historical Landmark by the National Historical Commission of the Philippines.
Reddish paintings on wooden panels commissioned by Father Antonio Ubeda from 1856 to 1859 are inside the church:The Ascension of Our Lord and Pentecost and two portraits of the Doctors of the Church. A third portrait belonging to the set of Doctors of the Church is on the church museum while the fourth portrait is lost. The paintings Agony in the Garden and Crowning of Thorns, is currently housed at the San Agustin Museum in Intramuros, Manila. The works of art are done by Liberato Gachalian.
Most ceiling paintings were unpreserved, an original work of Max Aya-ay in 1957 can still be seen on portions of the crossing.