Typical of small rural villages, Manikata had its own small church, since the parish of Mellieha was too far away to cater for the religious obligations of the farming community. It was towards the beginning of the 20th century, as the small community continued to increase, that a decision was taken to collect money to build a small church. The church was built in 1920, and was dedicated to St Joseph. As the rural settlement of Manikata formed part of various other parishes, the then Bishop of Malta entrusted the church to the Franciscan Conventual Friars, who were responsible for the parish of St Paul’s Bay, of which part of Manikata was part of.

The architect of this first church in Manikata is not known.  The church is typical of small rural churches that can be seen all over the islands. The façade has a central doorway with two small windows on each side for devotees to have the possibility of saying a prayer even when the church is closed for services. A small niche in the upper part of the façade, has a stone statue of St Joseph holding the Infant Jesus. 

Due to the ever-growing population of Manikata a larger church was built, leading to the eventual abandonment of the first church. The village was erected into a separate parish in 1975.