The Beginnings (1682 – 1690) 
The Carmelite Missionaries, who were sent to Malabar by Pope Alexander VII in the year 1657, started a small Seminary at Verapoly in 1682. The Seminary worked satisfactorily for some time, but it had to be closed down owing to some adverse circumstances.

The Re-organized Seminary (1764 – 1886
On 14th September 1764, the Sacred Congregation of Propaganda Fide wrote to the Vicar Apostolic of Verapoly asking him to re-open the Seminary at Verapoly for the formation of both the Latin and the Syrian Clergy. As the small seminary buildings at Verapoly could not accommodate all the seminarians, those of the Syrian Rite were lodged for some years at Alangad, under the supervision of the Carmelite Fathers. In the year 1774, however, we find both Syrians and Latins in the Verapoly Seminary. 
The Central Seminary at Puthenpally (1866-1932) 
The Seminary at Verapoly was shifted to the new buildings at Puthenpally in the year 1866. In 1888 the Seminary of Puthenpally was constituted the Major Central Seminary for the whole of Malabar, and was placed under the immediate jurisdiction of the Sacred Congregation of Propaganda Fide. Important changes were made in the curriculum of studies as demanded by the exigencies of time and circumstances. It was during this time that the study of languages such as Sanskrit, Greek, Hebrew and Malayalam was introduced in the curriculum. 
The Central Apostolic Seminary at Mangalapuzha, Alwaye (1932) 
Owing to the increase in the number of students at Puthenpally, a new seminary with better accommodation was built at Mangalapuzha, Alwaye. On 1st June 1932, the Theological Section was transferred from Puthenpally to the new Seminary, which was still under construction. In December of the same year, when more accommodation was made available in the new Seminary, the Philosophy Section too was transferred to Mangalapuzha. The official inauguration of the new Seminary was performed on 28th January, 1933 by the Most Rev. Leo P. Kierkels, C.P., the then Apostolic Delegate of India. The Seminarians at that time numbered 274.  On 2nd January 1951 took place the blessing of the newly constructed chapel of the Seminary.

The increase in the clerical vocations necessitated further extension. An adjacent hillock was bought and the new building constructed on it and it was to become the new Philosophical Seminary, named “St Joseph’s Apostolic Seminary, Carmelgiri”. On 24th November 1955 His Excellency the Most Rev. Martin Lucas, the then Apostolic Internuncio to India blessed and inaugurated it.

St. Joseph’s Pontifical Seminary   
In 1964 the Seminary was raised to the ‘Pontifical Status’ by the Holy See. His Excellency the Most Rev. James Robert Knox read the Papal Brief at a public meeting in the Seminary on June 14, 1964.

K.C.B.C. Entrusted with the Direction and Administration of the Seminary 
The Carmelite Order continued to administer the Seminary until its transfer to the Kerala Catholic Bishops’ Conference on June 12, 1976. On October 27, 1973, a formal request for the transfer of the seminary was made by the Superior General of the Carmelite which was approved by the Congregation for the Oriental Churches and the Congregation for the Evangelization of Peoples. The Statutes of the Seminary made by the two Congregations state that “St. Joseph’s Pontifical Seminary is a pluri-ritual Institution, common to the three Rites, namely the Syro-Malabar, the Latin and the Syro-Malankara”. It was also stated that “ the Seminary belongs to the Holy See and that its direction and administration is entrusted to the Conference of the Bishops of the three Rites of the Kerala region, subject to the high authority of the Sacred Congregation for the Oriental Churches and the Sacred Congregation for the Evangelization of the Peoples”. 

The Church of Kerala is greatly indebted to the dedicated missionaries of the Carmelite Order for the excellent formation they imparted to the clergy of Kerala for three centuries and more. It is a matter of great joy and honour for the Seminary that the cause for the beatification of two of its Professors, Fr. Aurelian O.C.D., and Fr. Zacharias O.C.D. has been taken up. Fr. Aurelian had served the Seminary for 51 years and Fr. Zacharias, for 45 years.

Pontifical Institute of Theology and Philosophy 
On February 24, 1972, the Congregation for Catholic Education issued a decree erecting a Theological Faculty in the Pontifical Seminary, Alwaye. The further history of the Faculty is given in the calendar of the Pontifical Institute of Theology and Philosophy, Alwaye. 

Carmelgiri: Major Seminary for the Latin Rite Community 
In compliance with the request of the K.C.B.C., made on June 5, 1995, for separate campuses on the basis of Rites, the Holy See has, without prejudice to the Pontifical Institute, Alwaye, which remains common to all the three rites, issued its nihil obstat by Prot. 4368/96, dated October 7, 1996, to re-organize St. Joseph’s Pontifical Seminary, Alwaye. As per the above decree, in view of promoting better formation in matters of Liturgy, spirituality and tradition of each sui iuris Church,  the Carmelgiri campus was assigned to the Latin Rite. 

Construction of the New Theology Block 
The new situation necessitated the various constructions. The construction of a three-storied building with a plinth area of 7630 Square metres took four years of construction works until it got completed toward the end of May 2002. 

The New Theology Block was blessed by His Excellency Archbishop Lorenzo Baldisseri the then Apostolic Nuncio to India on Sunday, June 2, 2002. The blessing was followed by a beautifully prepared solemn concelebrated Holy Mass in which the Apostolic Nuncio was the main celebrant. In the vote of thanks Msgr. Joseph Etturuthil, Rector bowed down in gratitude before the Almighty God for the great gift of the new theology block and thanked warmly all those organizations and persons who contributed generously to the realization of this beautiful dream of the Latin Catholics of Kerala State. He recalled gratefully the contributions of the Missio Bregenz, the Pontifical Works of St. Peter the Apostle, the Archdiocese of Köln, the Aid for the Church in Need, and the Italian Bishops’ Conference. The Rector thanked in a special way the Archbishop Lorenzo Baldisseri, Archbishop Daniel Acharuparambil who conceived the idea of the new building and guided through it, all the bishops of the Latin Hierarchy who firmly stood behind the Archbishop, the former Rector, Bishop Stanley Roman who saw through the different stages of construction and everybody former Rector, Bishop Stanley Roman who saw through the different stages of construction and everybody who helped him. All the members of the Staff and Seminarians worked very hard to make the day an unforgettably glorious day of Carmelgiri Seminary. Ten members of the Staff and one hundred and ten Theology students moved into the New Theology Block.  

Blessing of the New Kitchen and Refectory in the New Theology Block  
The long cherished dream of having a well equipped and well furnished new kitchen and refectory in the New Theology Block became a reality. Tuesday, August 12th, 2003 His Excellency, Rt. Rev. Dr. John Thattumkal, the Bishop of the Diocese of Cochin and member of the Episcopal Commission for the Seminary blessed the new kitchen and refectory and lighted up the flames of the new hearth. The new kitchen and refectory became fully operational on Monday September 1st, 2003. 

The Solemn Blessing of the New Chapel and the Assembly Hall 
The long awaited dream of having a beautifully furnished chapel and an Assembly Hall in the New Theology Block became a reality, the third year after the solemn blessing of the New Theology Block. Wednesday, August 4th 2004, the Solemnity of St. John Maria Vianney, the heavenly patron of the diocesan priests will ever be remembered in the annals of the history of our Seminary as the day the New Chapel and the Assembly Hall was solemnly blessed. In a most beautifully prepared liturgical celebration, His Grace, Archbishop Dr. Daniel Acharuparambil, the President of the Kerala Region Latin Catholic Bishops’ Council and the Chairman of the Episcopal Commission for the Seminary officiated a concelebrated Holy Mass and solemnly blessed the Chapel, and His Excellency, Rt. Rev. Dr. John Thattumkal, Bishop of Cochin gave a meaningful and exquisite homily.

 After the solemn blessing of the Chapel the senior most Bishop of the Kerala Region Latin Catholic Bishops’ Council, His Excellency, Rt. Rev. Dr. Mathias Kappil, the Bishop of Punalur presided over a short liturgical celebration during which he solemnly blessed the new Assembly Hall.

Solemn Blessing of the Marian Statue and the New Garden 

Devotion to the Blessed Mother is an integral part of the priestly formation. The magisterium of the Church, in particular that of the Holy Father John Paul II and illustrious lives of the Carmelite Missionaries have imparted such legacy to us. 

Keeping this in mind, the month of May dedicated to tender Marian devotion was concluded in the Seminary with the solemn meditated and devout recitation of Marian Rosary at the Marian Statue in the front garden of the old building of the Seminary. It was followed by a liturgical procession of all the students and Staff of the Seminary with lighted candles at the accompaniment of the melodious and devout singing of the Marian Litany to the newly erected Marian Statue in the front garden of the new Theology Block. His Grace Archbishop Dr. Daniel Acharuparambil blessed the Marian Statue and the new garden, and gave an inspiring homily on Marian devotion to be cultivated by every seminarian. Those who live in the theology block gather together on Saturday evening in front of the statue for a devout recitation of the holy Rosary. 

The “Bible Land” Relief Map 
The entrance of the Carmelgiri Campus is now beautified with a relief map of the Holy Land. It is a practical help for the students who learn the Holy Scriptures and it has become an attraction to the many who visit the Seminary. H.E. Rt. Rev. Stephen Athipozhiyil, the Bishop of Alleppey and member of the Episcopal

Commission for the Seminary blessed and opened the “Bible Land” for the public on 26th February 2009. 

The Meditation Chapel 
A quiet room at the top floor of the Seminary is set apart and is ideally furnished for meditation. The serene atmosphere compounded by the icon of Jesus provides a conducive atmosphere for personal prayer and meditation for those who desire solitude and pause from the routine hurry. 

In this connection,  we remember with eternal gratitude the Pontifical Works of St. Peter the Apostle, the Missio Bregenz, the Archdiocese of Köln, the Aid for the Church in Need, the Italian Bishops’ Conference who made very remarkable and generous financial assistance towards the construction of the New Theology Block. In a particular way, we are very much indebted to Rt. Rev. Msgr. Piergiuseppe Vacchelli and the Italian Bishops’ Conference who gave us a substantial financial assistance in furnishing and equipping the new kitchen and the refectory and the new Chapel and the Assembly Hall. We also remember with great indebtedness Fondation Baillairge, Canada and Pontifical Mission Societies, Malta. We most earnestly beseech the Lord to shower His choicest blessings upon each and everyone of them and the dear benefactors and benefactresses of these organizations.