While Fr. John Mary Chin, OCD, and his companions were searching for a place to live following the establishment of the Carmelite foundation in 1996, Archbishop Gregory Yong generously offered the community the use of his country residence on Punggol Seventeenth Avenue. In Divine Providence, this temporary residence was located on the very same street where the Carmelite formation house would later be established.

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As Carmelite spirituality began to take root in Singapore, several young men discerned a vocation to the Discalced Carmelite Order. In response to this growth, and during the tenure of Fr. John Chua as Delegate Provincial, the friars, with the generous support of benefactors and friends, purchased a bungalow in Sembawang in July 1999. On 14 December 1999, the Solemnity of St. John of the Cross, Archbishop Gregory Yong blessed the newly acquired house and dedicated it to St. John of the Cross, placing the formation of future Carmelites under the guidance and protection of the great Carmelite mystic and Doctor of the Church. 

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 On 1 April 2000, the house officially became the formation house for postulants from Singapore, Malaysia, Thailand, Myanmar, and Taiwan. To oversee this growing community, Fr. Tom Curran, OCD, was appointed the first House Superior and entrusted with the formation of the young friars.

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At that time, the formands travelled daily from Sembawang to St. Francis Xavier Major Seminary in Punggol for their philosophical and theological studies. As vocations increased, the Sembawang house soon became too small to accommodate the expanding community. A decision was therefore made to relocate the formation house closer to the seminary. With the assistance of generous benefactors and a loan from Archbishop Nicholas Chia, the friars sold off the old house in Sembawang and purchased two adjoining houses on Punggol Seventeenth Avenue in 2001. By 29 December 2001, these became the new St. John of the Cross Formation House, serving as the principal house of formation for friars preparing for Solemn Profession and eventual ordination.

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In its early years, the formation house accommodated postulants, novices, and simple professed friars pursuing their seminary studies. During his canonical visitation in 2007, the Superior General of the Order, Fr. Luis Arostegui, OCD, requested that the novitiate be established in a separate house to provide a more suitable environment for the canonical novitiate. Consequently, the novitiate was transferred to Tugbok, Davao, Philippines. Since then, the novitiate has ordinarily been held in the Philippines, with a few notable exceptions: Singapore (2010), Hsinchu, Taiwan (2013–2018), back to the Philippines (2019), temporarily returning to Punggol, Singapore (2020–2021) during the COVID-19 pandemic, and finally returning once again to the Philippines, first in Davao and presently in Malaybalay from 2024 onwards.

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Today, the St. John of the Cross Formation House continues to serve as the principal house of formation for the Singapore–Thailand–Malaysia Commissariat, preparing young friars to embrace the Teresian Carmelite vocation through a life of contemplative prayer, fraternity, study, and pastoral formation.