In 1979, God gave him Sis. Joyamma of Brethren faith as his helpmate. During those days, he realized the need for Salvation in Christ through the message of Vakathanam Podikunju Upadesi, a prominent revival speaker. It was during these days that the Holy Spirit filled both of them. The Lord gifted them with several spiritual gifts and slowly many doors for the expansion of the ministry was being opened. However, the fear of being isolated from the Church made Pastor Varghese, in 1986, get water baptized in secrecy.

Once while at work in 1987, Pastor Varghese was struck by a severe headache and he laid his head on his desk. Suddenly he heard someone echoing the scripture from Isaiah 40:3, “The voice of him that crieth in the wilderness, Prepare ye the way of the Lord….”. Hearing this he raised his head with complete deliverance from his discomfort. He shared this experience with his Christian colleagues who told him that this was nothing but God's clear call. In 1988, Sis Joyamma also received the divine call from above.

Meanwhile, the powerful messages of Vaylathala Avarachan, Pastors M. Abraham, K.C. John and a few others made clear the mystery of the scriptures and the Truth in it. Pastor Varghese realized the need for complete separation and a clear definite doctrinal standpoint, and thereby left his traditional Marthoma faith and fellowship.

In 1989, along with Pastor P.J. Samuel (Asst. Financial Controller of the Sheraton Hotel) as Chief Pastor, Pastor Varghese as the Associate Pastor and Church Secretary, and a few others worked together in the formation of an independent Church. Later the Church was affiliated to the largest indigenous Church in India, the Indian Pentecostal Church of God (IPC). By God's grace the Church today stands strong with over 400 spirit filled members as the Full Gospel Church of Kuwait (FGCK), growing day by day.

Meanwhile, the Gulf War in 1990 still remains a dark chapter in the life of Pastor Varghese and his family. The family, who with many others, lost all their belongings and returned to India as refugees. However, after stability to the crisis in the Gulf, both of them were called back to Kuwait. Nevertheless, the constant and continuous burden for entering into full time ministry forced the couple to resign their jobs and left Kuwait for good in 1992.

While in Kerala, Pastor T.E.Varghese assisted Pastor K.C. Thomas (Currently IPC Kerala State Secretary) and later completed theological studies at Hebron Bible College (now India Bible College). Nevertheless, strong guidance of the Holy Spirit led the family, in 1993, to take base at Chathannoor in the District of Kollam, Kerala.

In 1994, taking into heed the guidance and advice of senior pastors of IPC, Pastor Varghese was ordained as the minister of the local church of around 25 members at Karamcode under Kollam South Centre. Under the leadership of this church several out station works were begun. Gradually, several leaders of the IPC advised Pastor Varghese to take charge of these churches and form a Centre. Prominent among them was Pastor John Richard (IPC Kollam South Centre Minister) whose words were a great encouragement and boost to the ministries at Chathannoor. These were later coordinated together and the IPC Kerala State Council sanctioned it as IPC Chathannoor Area which was later upgraded to as the IPC Chathannoor Centre in 2001. Today the Centre has 9 Local churches and 2 out stations with a total of around 400 members.

His wife, Mrs. Joyamma Varghese shares his passionate commitment to the Lord and is the key helper of the ministry. She is also a renowned Bible Teacher at different Ladies' Bible Institutes. Together they have two children, both having dedicated their lives for the Lord's ministry.