The gospel was brought to what is now Bavaria by Boniface and other missionaries in the 8th century. The Lutheran Reformation was fully established in Nuremberg by 1524. In 1530, the city of Augsburg gave its name to the major Lutheran confession. The Religious Peace of Augsburg (1555), laying down the principle that the religion of the ruler determines the religion of his subjects, and the rise of the Counter-Reformation, had the effect that more than half of the Lutherans in Bavaria returned to the Roman Catholic Church. The actual founding of the Evangelical Lutheran Church in Bavaria took place in 1803.

The largest local ecumenical partner of the ELKB is the Roman Catholic Church. Among other partners are Orthodox churches, of which many members are migrant workers, followed by Old Catholics, the Evangelical-Reformed Church and Evangelical Free churches of various traditions. A particular concern is the provision of church services for tourists. The peace question and work on transforming economic globalization are high on the agenda. The church continues to seek and strengthen ecumenical fellowship with other churches through a variety of programmes and activities. It maintains special relations with Evangelical Lutheran churches in Papua-New Guinea, Tanzania, Brazil and Hungary, and with Orthodox churches in Russia and Iraq.