The shape of its roof resembles a salakot, a traditional Filipino hat used by farmers and fishermen in their respective agricultural activities as their protection against the heat and rain.

Inside the main church hangs a huge replica of the Glorious Cross derived from the design used for the Archdiocese of Lipa during the Jubilee Year 2000.

The cross at the crucifix, the bottom of the altar table and the lectern are made of drift wood to adapt to the design of the main church.

The rector and parish priest Joselin C. Gonda envisioned this concept for the main church, to have a place of worship and prayer that is distinctly Filipiniana, eco-friendly and adapted to the tropical climate of the site surrounded by a very green environment, making it a unique, serene and welcoming atmosphere drawing pilgrims to pray, to reflect and to be inspired by God and the nature God created.

Other designated pilgrimage churches were San Sebastian Cathedral, Carmelite Monastery, Redemptorist Church and the Archdiocesan Shrine of San Vicente Ferrer in Lipa City, Minor Basilica of the Immaculate Conception and the Most Holy Trinity Parish in Batangas City, and Basilica of St. Martin of Tours and the Archdiocesan Shrine of Our Lady of Caysasay in Taal.

[5] On September 23, 2013, the feast day of Saint Padre Pio of Pietrelcina, the main parish church was dedicated to God by Cardinal Gaudencio Rosales.

[6] On September 14, 2015, marking the first day of novena to Saint Padre Pio, the president of the CBCP and Lingayen-Dagupan archbishop, Socrates Villegas, led the solemn declaration of the national shrine.

After reading the Gospel followed by a brief homily, prayer for healing of the sick comes when first- and second-class relics of Padre Pio are exposed to be venerated by the pilgrims.

It is said that a woman named Vittoria had a vision of luminous rays formed by thousands of white and red roses that radiated out from Padre Pio and spread in every direction.