Tradition pinpoints that Augustinian missionary priests were the first to administer the district of Biñan until 1637, when the Dominican Fathers took over. At the end of the 18th Century, secular priests took charge of the parish. Its first appointed parish priest was Fr. Jose Monroy in 1757. 

An earthquake in 1826 and 1880 destroyed the parish church and convent. Construction of the new church began in 1892, initiated by Fr. Rafael Pajol, a Dominican priest. It was only on May 13, 1929, when the construction of the present belfry was finished. The old church was remodeled around 1953 but was burned in 1962. Another fire destroyed it in 1968 and it was reconstructed under the leadership of Mayor Jesus Garcia. 

Other more improvements were made in the succeeding years. On September 9, 2019, the parish church was solemnly dedicated by Bishop Buenaventura Famadico. Owing to the historical significance of the church and the small original wooden image of the patron San Isidro Labrador, the parish church was elevated into the status of a Diocesan Shrine on May 6, 2022. 

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