Warrior Nun features a central, affirming romantic relationship between its two female protagonists, Ava and Beatrice. Their love story is developed with dignity and complexity, serving as a significant emotional core and source of strength. The portrayal is overwhelmingly positive, depicting their queer identity as an integral and respected aspect of their characters.

The show features several female characters who engage in and win close-quarters physical combat against male opponents. Sister Beatrice demonstrates martial arts and staff fighting prowess, while Ava Silva utilizes enhanced physical abilities and hand-to-hand combat to overcome male adversaries.

The character Julian Salvius, a male scientist in the original comic series, is portrayed as Jillian Salvius, a female scientist, in the show adaptation. This constitutes a gender swap for a significant character.

The show adapts characters from the "Warrior Nun Areala" comic series. Several key characters, such as Sister Lilith and Sister Beatrice, who were depicted as white in the original comics, are portrayed by Black and biracial actresses, respectively, in the show.

The show portrays the Order of the Cruciform Sword, a Catholic-affiliated group, with respect for their faith, dedication, and fight against evil. While acknowledging institutional flaws, the narrative aligns with the virtues and dignity of the faith, presenting it as a source of strength and purpose.