Foreseeing difficult and confusing times, the EELC General Synod passed a resolution in 1943 where "the EELC archbishop is authorised, in case the EELC General Synod or the EELC Consistory is not able to hold a meeting, to make decisions on behalf of the EELC General Synod or EELC Consistory which will have the same authority as if they had been made by the EELC General Synod or the EELC Consistory". On the basis of this authorisation, Archbishop Johan Kõpp founded in Stockholm the Estonian Evangelical Lutheran Church Committee. This was the beginning of orderly functioning of the EELC abroad, registering of congregations in Stockholm, the centre of church life. Using the same authorisation, the EELC, under the leadership of bishop Kõpp, takes part in the founding congress of the Lutheran World Federation in Lund in 1947, where the EELC is put down in the founding members' list. The same occurs next year in Amsterdam where the World Council of Churches is being established.

On 31 June 1947, bishop Kõpp sent a circular to all the pastors of registered congregations, one part of which says: "The general attitude of the exile church should be that the Estonian Evangelical Lutheran Church is essentially one and the same church and although it is temporarily split up into many parts, it has the same basis for teaching and follows the EELC Statutes as strictly as possible in any given situation. Congregations, religious groupings or unions should all come together and form districts in order to serve their fellow countrymen in their religious need."
In addition to the above-mentioned circular, the exile EELC's general work principles were soon written down and distributed between congregations. The principles stressed that the EELC in exile is an independent self-governing church which functions on democratic grounds, calls together congregations, ordains the pastors, holds services and carries out religious ceremonies according to the Service Book, the Statutes and the established order. One of the main aims is to proclaim the Gospel in the Estonian language and maintain the church of our forefathers for the future when we can hand it on to the next generations, sound and unified both outside and inside, and not split up into many different parts.

On 30 January 1957, relying again on the authorisation given to him in 1943, bishop Kõpp decides to replace the word 'bishop' with the word 'archbishop', and 'assistant bishop' with 'bishop'. In 1953, the EELC congregations began to unite into deaneries. According to the decree of the Consistory, the first deanery was established in England, then in Sweden, and in late 1953 also in the USA. The Chicago deanery in the USA was established in 1954. During the '70s, deaneries were formed in Canada, Germany and Australia. In 1976, Canadian dean Karl Raudsepp is ordained the EELC bishop, with special mission in North America.

It is also decreed that the General Synod pass resolutions by written votes, where each congregation has one vote. The EELC Consistory or church government is officially established, always located at the archbishop's residence. Archbishop Johan Kõpp became emeritus only a few months before his 90th birthday, and on 26 May 1964, bishop Johannes Oskar Lauri was elected the new archbishop. The Consistory remained in Stockholm, and a number of assessors from Sweden and USA also belonged to it. They take upon themselves the difficult task of compiling the code of church laws that would contain all rules and regulatory norms concerning church work that were approved between 1933 and 1980. The result was "The Church Law Handbook" which introduces the rules of functioning of Estonian people's church in exile. This publication has been well received and recognised in many countries and world organisations where the EELC is considered as a lawfully functioning church.
Archbishop Johannes Lauri retired from office before his 80th birthday and on 6 December 1971, the EELC General Synod appointed Konrad Veem, pastor of the Stockholm congregation and assistant dean of the Swedish deanery as the new archbishop. He was ordained on 18 June 1972 in the Stockholm St.Jacob's church.

Huge distances where the area of one congregation has been almost the size of Estonia itself have hindered the work of the Estonian Evangelical Lutheran Church and its congregations. But the work has been made easier by our firm conviction that we want to be and are Estonians who belong to the Estonian church. When during 1948 - 1951, many Estonians moved on from Sweden, England and Germany mainly to the cities and villages of North America, the local congregations and churches insisted that our people should join their Lutheran congregations. Estonians declined their offer and immediately began to establish congregations in their mother tongue. After a while when the local congregations saw that the Estonians were quite determined in their wish, they helped to finance the buying or building of new churches. Estonian congregations belonged to Estonian churches but at the same time they indirectly belonged also to the churches of their country of residence. This gave our church a legal status in those countries. Nevertheless, the EELC retained its Statutes, which in reality did not much differ from that of other Lutheran countries.
It is not possible here to enumerate all publications that have been produced over the years. At first it was essentially necessary literature: for children, young people, confirmands, religious textbooks, Martin Luther catechism, prayer books for the young etc. In addition, collections of sermons and exegeses were published. The Consistory newspaper "Estonian Church" has appeared without interruption until today.

Sixteen people have obtained theological education in universities and seminaries of their resident countries. Four-five of them began to serve local congregations but the majority went to work in the EELC congregations. The EELC set up a Theological Institute, which initially operated in Stockholm, and since 1978 in Toronto. At the head of the Institute have been Dr. Arthur Võõbus, Bishop Karl Raudsepp, Tõnis Nõmmik (AM) and Dr. Andres Taul. In recent years, some lecturers have come from Estonia. 21 pastors have been ordained at the Institute. The total number of new pastors in Estonian exile church is 37.

Archbishop Konrad Veem retired in 1990. On 1 September 1990 the EELC Church Council elected Udo Petersoo, the dean of Canada and pastor of the Toronto St. Andrew's congregation to replace him.
The EELC today has about 15 700 members who are divided into 63 congregations and who are served by 34 pastors.