The anonymous libretto draws on existing works (notably by Barthold Heinrich Brockes) and is compiled from recitatives and choruses narrating the Passion of Christ as told in the Gospel of John, ariosos and arias reflecting on the action, and chorales using hymn tunes and texts familiar to a congregation of Bach's contemporaries.

He chose the chorales: For the words of the aria "Ach, mein Sinn" (#13), Bach used an adaptation of a 1675 poem by Christian Weise, "Der weinende Petrus".

[9] For the central chorale (#22) "Durch dein Gefängnis, Gottes Sohn, muß uns die Freiheit kommen" ("Through Your prison, Son of God, must freedom come to us) Bach adapted the words of an aria from the Johannes-Passion of Christian Heinrich Postel (1700) and used the melody of "Mach's mit mir, Gott, nach deiner Güt" by Johann Hermann Schein.

The architecture of Part Two shows symmetry around this movement, the music of the preceding chorus #21f "Wir haben ein Gesetz" corresponds to #23b "Lässest du diesen los", the demand #21d "Kreuzige ihn!"

[12] Alternate numbers that Bach introduced in 1725 but later removed can be found in the appendix to scores of the work, such as that of the Neue Bach-Ausgabe (and heard in the recording by Emmanuel Music directed by Craig Smith, cited below).

33 reads "Und die Vorhang im Tempel zerriß in zwei Stück; von oben an bis unten aus."

[16] In 1725, Bach replaced the opening and closing choruses and added three arias (BWV 245a-c) while cutting one (Ach, mein Sinn) from the original version.

[13] The opening chorus was replaced by O Mensch, bewein dein Sünde groß, which was later transposed and reused at the end of part one of the St Matthew Passion.

[citation needed] Overall, Bach chose to keep the biblical text, and inserted Lutheran hymn verses so that he could return the work to its liturgical substance.

[20] In 1749, he reverted more or less to the original of 1724, making only slight changes to the orchestration, most notably replacing the by-then almost obsolete viola d'amore with muted violins.

[22] Fred Wolle, with his Choral Union of 1888 at the Moravian town of Bethlehem, Pennsylvania, was the first to perform the St John Passion in the Americas.

[25] Bach proved that the sacred opera as a musical genre did not have to become shallow in liturgical use by remaining loyal to the cantus firmus and the scriptural word.

[20] The text for the opening prayer, "Herr, unser Herrscher, dessen Ruhm", as well as the arias, chorales and the penultimate chorus "Ruht wohl, ihr heiligen Gebeine", come from various other sources.

[27][better source needed][28] More recently, the tradition of including the St John Passion in a full-scale Good Friday service was revived in Kokkola, Finland in 2023.

[33] Lukas Foss, who came to the United States in 1937 as a Jewish refugee from Nazi Germany, changed the text from "Juden" to "Leute" (people) when he conducted performances of the work.

[32] This has been the trend of numerous mainline Christian denominations since the late 20th century as well, for instance, the Episcopal Church, when they read the gospel during Good Friday services.

He also noted that Bach used words for the commenting arias and hymns that tended to shift the blame for the death of Jesus from "the Jews" to the congregation of Christians.