The history of the ELCM can be traced back to the large scale immigration of Indians from the Tamil speaking areas of India from the 19th to 20th century to British Malaya as cheap labourers in plantations.

Among the many migrants were Tamil Lutheran Christians from churches started by the work of the Danish-Halle Mission and Bartholomäus Ziegenbalg.

Thiruchilluvai Joseph immediately set about organising the Tamil Lutherans for regular divine services, the first of which was held on 30 January 1907 in a shop house at Scott Road off Brickfields in Kuala Lumpur.

Simultaneously, the Leipzig Mission also assigned Ratnam, a school teacher turned catechist, to assist the work in the Penang area.

1908 —Following K. Pamperrien's visit, the Leipzig Mission in India showed greater interest in Malaysia and launched a constructive programme of development for the spread of Lutheranism.

1909—On 2 June a piece of land was purchased for construction of Zion church with money contributed by Leipzig Mission.

The enormous task of providing pastoral care for the Tamil Lutherans nationwide became the responsibility of Rev Thiruchilluvai Joseph, who was based in Kuala Lumpur.

On 30 November 1924, J. Sandegren dedicated the Zion Church building (President of the CSM in South India, later third bishop of Tranquebar).

While the Swedish mission and the TELC order was partial to an episcopal polity, it was not accepted by the American missionaries who felt that the local Chinese Lutherans would not be familiar with that form of government.

There were also disagreements on the nature of apostolic succession as well as the significant differences in the culture, language and origins between the Tamils and Chinese who were ministered by the respective missions, the former consisting mainly of established Tamil Lutheran families while the latter consisted mainly of congregations of young individual Chinese who were first generation Christians.

The ELCM pioneered work among people suffering from epilepsy when it set up a training centre for epileptic children in Hutan Melintang, Perak known as Bethany Home in the 1966.

Due to the historical heritage of the ELCM, Tamil and English remains the primary language of ministry and liturgy in the church, but the use of Malay has been increased over the last decade.

ELCM congregations have been centres for pre-school education since the beginning and was a founding member of the governing council of Seminari Theologi Malaysia.