During this same period the Rector's Garden was redesigned to improve drainage and accommodate a columbarium and the belltower was refitted for a carillon of fifteen bells, cast by Fonderie Paccard of Lac d'Annecy, France.

In 2003, the then-dean Paul F. M. Zahl hung a black flag on the cathedral in protest of the election of Gene Robinson as the first openly gay bishop in the Episcopal Church.

[8] From 2013 to May 16, 2021, the dean and rector was the Very Reverend Andrew C. Pearson Jr.[9] In 2019, the search committee for the new bishop identified the beleaguered relationship as one of four major challenges facing the diocese.

In June 2021, the Advent and the diocese affirmed a new covenant recognizing the cathedral’s commitment to a Protestant, evangelical expression of Anglicanism and stating that the it would return to the use of the 1979 Book of Common Prayer (Rite I) for its principal services.

[15] Strains between the Advent and the diocese again became public in December 2021 when the diocesan bishop, Glenda Curry, ordained four individuals to the priesthood at the cathedral one of whom was in a same-sex marriage.

When this detail was made public by conservative Anglicans, cathedral leaders complained that the bishop had not told them of the individual's status.