Very early, the region of Alsace-Moselle embraced the ideas of the Reformation. Already in 1521 the theses of Luther were defended in the Cathedral Church of Strasburg, which became an important centre of the Reformation movement through the activities and stories of Martin Brucer. The Protestants of Strasburg were followers of Luther. Jean Calvin had stayed in Strasburg. Metz, Mulhouse, and other cities in the region adhered to the “reformed” stream (Calvinistic or Zwinglian). That history of separation is at the origin of the distinction between the ECAAL (Lutheran) and the Reformed Church of Alsace and Lorraine (ERAL). Today, the two churches have come close to one another and are in close cooperation. The particular confessional status foreseen by the Treaty of Westphalia (1648) made the implementation of the Revocation of the Edict of Nantes (1685) impossible in this region. In 1905, the region was under German rule and hence was not concerned by the separation of church and state. In other words, Alsace-Moselle was not affected by the two major turning points in the history of French Protestantism. As a result, the pastors (like the priests and rabbis) are paid by the state and religious instruction is given in the schools.

The ECAAL adheres to the creeds of the early church, the Confession of Augsburg and the Small Catechism of Luther. The church is organized in 40 consistories and seven inspections (synods). The highest governing bodies are the consistory and the directory, the executive organ. The church represents about 20 percent of the Protestants in France and 14 percent of the population of Alsace, whereas Protestants form only two percent of the total population of France. By virtue of their geographical situation, the Protestant churches of Alsace and Moselle play a bridging role between the Protestant minorities of southern Europe and the Protestant majority churches in the North of the continent.

The ECAAL participates in the witness and service of other Christian churches in the world, and strives to deepen the communion and cooperation of the churches. Besides belonging to the French Protestant Federation, the CEC, the WCC and the LWF, it is a member of the Permanent Lutheran-Reformed Council and of the National Alliance of Lutheran Churches in France, of the Communion of Protestant Churches in Europe (Leuenberg) and presides over the Conference of Churches on the Rhine, which is a grouping of 21 churches in France, Germany, Austria, the Netherlands and Switzerland.

In 2006 the ECAAL and the Reformed Church of Alsace and Lorraine established the Union of Protestant Churches of Alsace and Lorraine (UEPAL). The new body is not a united church but it provides a common decision making structure and a single body of pastors.