[4] In 1988 after the death of Joseph Höffner, Meisner was named Archbishop of Cologne, a post he continued to hold until he retired.

[5] In January 2013, two Catholic hospitals refused to provide a "morning after pill" to a rape victim based on Church policy that treats such medications as abortifacients.

Meisner apologized and approved the use of some such pills for rape victims based on the belief that they prevented fertilization and did not induce abortion.

[a][9][10] On 25 December 2013, Cardinal Meisner turned 80 and lost the right to participate in future conclaves and he submitted his resignation, which Pope Francis accepted on 28 February 2014.

[11] Diocesan administrator Stefan Heße led the archdiocese until a successor, Rainer Woelki, was appointed on 11 July and installed as Archbishop on 20 September 2014.

His choice of words recalled the phrase "entartete Kunst" ("degenerate art") used as the title of the exhibition opened by Adolf Hitler in Munich on 19 July 1937 and provoked strong negative reaction.

[d] It was widely recognized that Meisner was criticizing the stained-glass window in Cologne Cathedral by Gerhard Richter, which was unveiled just weeks before and of which he disapproved.

Meisner and three other cardinals (Carlo Caffarra, Walter Brandmüller and Raymond Leo Burke) submitted dubia (doubts) in private, followed by a public letter ("Seeking Clarity: A Plea to Untie the Knots in Amoris Laetitia") in November 2016, asking Francis to clarify various points of doctrine.

The public letter asked about fundamental issues of the Christian life and referenced Pope John Paul II's encyclical Veritatis splendor.