The Diocesan Shrine and Parish of San Jose is thought to be the town of Navotas's first church.

On May 21, 1599, it was called Visita de Tondo, and was administered by Agustinian friars
before it changed its name. In 1771, the friars told the Navotas faithful to go to Mass in the
nearby town of Tambobong which made the Archdiocese of Manila issue a decree that made
the parish of San Jose de Navotas official. The parish was founded under the patronage of St.
Joseph on July 1, 1859. Fr. Matias Novoa, O.S.A., is the first parish priest at the church where
we live.

As time went by, in January 1860, the main retablo was done with the image of San Jose in the
center. After this, in December of 1860, the cemetery was built, as well as the belfry, which is
now known as the adoration chapel. The belfry was built with a bell dedicated to Saint Joseph
that weighed 46 arrobas, 16 libras, and 16 arrobas. It was donated by Cabeza Miguel Oliveros,
and his daughter, Agustina Augustine, was honored with the bell. On November 5, 1865,
Archbishop Gregorio Meliton Martinez y Sta Cruz paid his first pastoral visit. Padre Manuel
Perez O.S.A. completed the baptistry in May 1867 and began building of the new church in
January 1868 under his direction. He died on March 22, 1877, unable to see the church
finished. As a result, Padre Martin Ruiz, O.S.A., parish priest of San Bartolome de Tambobong,
was named temporary parish priest. Padre Gavino de los Reyes became the church's first
Filipino secular parish priest in March 1877. During his tenure, Archbishop Pedro Payo, O.P.,
made a visit. He was succeeded by Padre Guillermo Cuevas, who deliberately finished Padre
Reyes's October 22, 1877, extension of the church's construction.

Between July 15 and 20, 1880, a tragedy struck, destroying the convent and forcing the parish
priest to temporarily relocate to Capitan Juan Sioson's house directly across from the church.
Following recovery, construction on the convent ceiling was resumed. On March 2, 1889, Padre
Mariano Rivas, O.S.A., succeeded Padre Diez. He created the marble holy water fountain that
is still in use today. On June 20, 1891, Padre Tomas Agudo, O. S. A. came in this town as the
town's final Spanish parish priest. He commenced building the current parish church in June
1892. This is the church that the majority of Navoteos are familiar with and adore. Don
Florentino Andres donated a large image of St. Joseph standing in the cloud with angels as the
new church's altar was built. Padre Nicolas Avendao became the town's permanent and first
Filipino parish priest on December 1, 1898. He endured numerous confrontations and hardships
throughout his term, as the Aglipayan division developed following the American revolution and
invasion.

Eventually, Padre Pedro Ignacio took over as parish priest on November 2, 1952. On his watch,
the St. Joseph Parish Church Construction Project was established with the backing of San
Jose de Navotas Parish Council, which completed essential adjustments in compliance with
Second Vatican Council regulations. Msgr. Lorenzo Egos and the Parish Pastoral Council
started the "Bahay-Pari" and a multi-purpose center for parish events and activities during this
time period of the church's construction. Msgr. Jesus-Norriel Bandojo succeeded Msgr Rolando
dela Cruz on July 19, 1997, becoming the parish priest. A perpetual adoration chapel was built
during Bandojo's tenure because to the generosity of the Del Rosario family. The San Jose
Church Construction Committee was set up to manage the church's repairs and restorations.
The first bishop of Kalookan, Bishop Deogracias Iiquez, visited the parish in 2005 for the first
time. San Jose de Navotas Parish was designated a pilgrim church during the Year of Faith
commemoration of 2013. It was on December 8, 2015, when San Jose de Navotas Parish was
selected as a pilgrim church and the "Door of Mercy" was opened. Basic Ecclesial Communities
grew up all around the parish. On January 5, 2017, Fr. Rufino Yabut was named as the next
priest of San Jose de Navotas.