In 1905, Schweitzer began his study of medicine at the University of Strasbourg, culminating in the degree of M.D. in 1913.
The exposition of these ideas, encouraged by Widor and Munch, became Schweitzer's last task, and appeared in the masterly study J. S. Bach: Le Musicien-Poète, written in French and published in 1905. There was great demand for a German edition, but, instead of translating it, he decided to rewrite it. The result was two volumes (J. S. Bach), which were published in 1908 and translated into English by Ernest Newman in 1911. Ernst Cassirer, a contemporaneous German philosopher, called it "one of the best interpretations" of Bach. During its preparation Schweitzer became a friend of Cosima Wagner, then resident in Strasbourg, with whom he had many theological and musical conversations, exploring his view of Bach's descriptive music, and playing the major Chorale Preludes for her at the Temple Neuf. Schweitzer's interpretative approach greatly influenced the modern understanding of Bach's music. He became a welcome guest at the Wagners' home, Wahnfried. He also corresponded with composer Clara Faisst, who became a good friend.
In 1905, Widor and Schweitzer were among the six musicians who founded the Paris Bach Society, a choir dedicated to performing J.S. Bach's music, for whose concerts Schweitzer took the organ part regularly until 1913. He was also appointed organist for the Bach Concerts of the Orféo Català at Barcelona, Spain, and often travelled there for that purpose. He and Widor collaborated on a new edition of Bach's organ works, with detailed analysis of each work in three languages (English, French, German). Schweitzer, who insisted that the score should show Bach's notation with no additional markings, wrote the commentaries for the Preludes and Fugues, and Widor those for the Sonatas and Concertos: six volumes were published in 1912–14. Three more, to contain the Chorale Preludes with Schweitzer's analyses, were to be worked on in Africa, but these were never completed, perhaps because for him they were inseparable from his evolving theological thought.
At the age of 30, in 1905, Schweitzer answered the call of The Society of the Evangelist Missions of Paris, which was looking for a physician. The committee of this missionary society was not ready to accept his offer, considering his Lutheran theology to be "incorrect". He could easily have obtained a place in a German evangelical mission, but wished to follow the original call despite the doctrinal difficulties. Amid a hail of protests from his friends, family and colleagues, he resigned his post and re-entered the university as a student in a three-year course towards the degree of Doctorate in Medicine, a subject in which he had little knowledge or previous aptitude. He planned to spread the Gospel by the example of his Christian labour of healing, rather than through the verbal process of preaching, and believed that this service should be acceptable within any branch of Christian teaching.
Schweitzer was one of colonialism's harshest critics. In a sermon that he preached on 6 January 1905, before he had told anyone of his plans to dedicate the rest of his life to work as a physician in Africa, he said: