The Jesuits first landfall in Samar was a place called Tinago in the Municipality of Tarangnan in the year 1595. That same year, Francisco Otazo, SJ founded the Catbalogan mission. It became the principal mission on Samar’s western coast, when Tinagon was struck by famine and disease causing the Jesuits to abandon the area. This increased the importance of Catbalogan but it was vulnerable and subject to frequent seaborne attacks. During one such attack, the village was burnt and its Jesuit pastor killed. Three known martyrs of Samar were Gabriel Coronel who died 27 May 1627; Ignacio Zapata, died 8 Jan. 1666; and Francisco Angel, died 24 Feb. 1674 on Maripipi island (Redondo y Sendino, 94; HC  gives the year of Angel’s death as 1676).
In 1627, Catbalogan was raised to the status of residencia (residence or central house) and among its dependencies was Paranas (Wright) where in 1629 Fr. Pedro Estrada is reported as actively evangelizing the area.
The Annual Letters of 1631–32 report that because a fort was constructed in Catbalogan and the townspeople could now live in peace near the fort. Annual Letters were periodic reports which Jesuits superiors sent to Europe, to acquaint administrators in Rome and Spain of the status of the missions. Although they were meant to be dispatched every year to Europe, difficulties of sea travel made it such the letters were sent on the average every three years.
Aside from the fort, a stone house was constructed after three years of labor. In this house the altar of Our Lady was kept to protect it from typhoons. Obviously the church at this time was of light material as it could not protect so precious and expensive a thing as an altar.
According to Huerta the present stone church of Catbalogan was built prior to 1760. The date is based on the report that in 1760 or eight years before the expulsion of the Jesuits, this church was burnt. On 17 October 1768, Catbalogan was ceded to the Franciscans who received it from the Jesuits. The first Franciscan parish priest was Fray José Fayo. When the Franciscans arrived they found the Jesuits ministering to the spiritual needs of the people in a camarin (shack) of nipa, while the shell of the church, apparently saved from the conflagration, needed repair. Thus, since the fire the Jesuits did not have the resources to repair the church.
In 1769, José de Jesús Marín, OFM established an infirmary, but probably this building was also of nipa and bamboo.
The church did not assume its present from until in 1814, when Félix Carreón, OFM set out to repair the church. Martín de Yepes, OFM constructed the altars of Catbalogan. He also had a colonnade of wooden posts raised, thus dividing the nave into three. The façade used Ionic columns for its articulation.
In 1835, The church burnt a second time but was rebuilt by the Franciscans. (Redondo suggests that there was another fire between 1814 and 1835 [Redondo 1886, 216].)
Church—Records are unclear about the extent of damage on the church. Huerta implies that the stone fabric withstood the fire of 1760 that consumed all that was combustible. But the fire of 1835 must have left little of the Jesuit church. Add to that the devastation of World War II and we have little left from Jesuit times. If anything remains from Jesuit times, it might be the meter-high image of the patronal saint, St. Bartholomew, presently kept in the rectory.
Fort—Certainly parts of the fort behind the church trace to Jesuit times, Delgado’s description corresponds closely with what is left of the fort. Delgado’s words: “Catbalogan possesses a large fort, capacious and quadrilateral, and at the corners facing the sea two bulwarks with mounted artillery. The church and residence of the Fathers of the Society are built in the fortification. Two blockhouses were built at the landward corners of the fort. The fort is always well-provided with gunpowder, bullets and other weapons because of the present need. We are constantly under attack from all sides by Moro ships” (1754, 239-40).
It is not certain if Delgado is describing the fort mention in the Annual Letters of 1631–32, if so then the fortification behind the Catbalogan church is much older than the church. It could also be a later construction completed when the Jesuits built a stone church in Catbalogan.
Described by Delgado as “fuerza grande” with “muralla y baluarte” remnants of the fort walls and a stone blockhouse are found behind the Catbalogan church. The enclosed compound is now a provincial jail. Landor (1904: 444) indicates that by the early 20th century the fort was already a jail and that its walls were deliberately demolished. This means that the existing fortification at Catbalogan is part of a more extensive fortification that may have surrounded the church complex. Landor writes: “Catbalogan, also on the west coast of Samar, … was a biggish town, with a handsome church, a large fort (turned into the provincial jail), the wall of which had in great part been demolished. The town extended mostly to the east of the fort… To the west a bridge connected the town with a small hill on which were the remains of an old Spanish block-house—a position occupied later by the insurgents, who placed a piece of ordnance here.”
The Franciscans were responsible for other architectural initiatives. They built the cemetery and its chapel dedicated to the Blessed Virgin, possibly the casa real of stone and wood near the church. The lower story of the casa is now the Philippine Constabulary barracks. Dates of construction are uncertain.