Travelers and especially sailors would visit before leaving on a journey, and to pay their respects upon arriving back on land.

In the place that today occupies the church, in 1604 the congregants of the Third Franciscan Order, erected a modest hermitage called "Ermita del Humilladera" and had as its function the twelfth or final station of the Via Crucis.

In 1693 the temple was enlarged, rebuilt and converted into auxiliary of the Parochial Major Church by Bishop Diego Evelino de Compostela, who later elevated it to a parish in 1703.

The Iglesia Santo Cristo del Buen Viaje was the last station on the Stations of the Cross, a procession that started at the old St Francis church and proceeded to el Santo Cristo through Calle Amargura.

The hermitage was the twelfth station of the Vía Crucis (Procession of the Cross), which took place annually during Lent and led along Calle Amargura from the Plaza de San Francisco.