The small village of Għargħur once formed part of Naxxar until it became a separate parish in 1598. However, the chapel of St John the Baptist in Għargħur, which initially became the parish church of Għargħur, only received official recognition in 1610 after formalities were suspended through an objection that had been made.

As the congregation in Għargħur grew, the need for a larger church was felt.

It was decided to build a new parish church on top of the hill on the site of a small chapel dedicated to St Bartholomew.

Tumas Dingli was engaged to design the parish church and it was built between 1617 and 1638. The church is designed and built to a traditional Latin-cross plan, similar to Dingli’s other parish churches of Attard and Balzan, although smaller in scale.

Subsequently, the church underwent numerous changes with a major change coming around the year 1740 when the façade designed by Dingli was replaced with the one that exists today.

Although the architect who redesigned the façade is not confirmed, many however attribute it to Pietro Debono. Even though the church was restricted in width, Debono accentuated the vertical mass of the new façade by incorporating large order pilasters and the twin bell towers using a more ornate and elaborate Baroque style.

The Malta Environment and Planning Authority scheduled the parish church as a Grade 1 monument on August 26 as per Government Notice 782.