Major Crimes offers a predominantly positive portrayal of LGBTQ+ characters and themes. Key characters like Rusty Beck and Gus experience affirming arcs, including a loving relationship and marriage, depicted with dignity and complexity. The series consistently frames LGBTQ+ identities respectfully, with any obstacles or prejudice presented as external societal issues rather than inherent to queer identity.

Major Crimes features Alice Herrera, a transgender woman, as a witness in a murder case. The show portrays her with dignity and agency, with lead characters actively correcting misgendering and ensuring respectful treatment. Her identity is affirmed, and she is presented as a valuable contributor to the investigation, reflecting a positive and empathetic stance.

The series respectfully portrays Christian characters and often aligns its narrative's moral compass with virtues such as justice, compassion, and redemption, which are central to Christian ethics. While not overtly religious, the show generally depicts Christian faith as a source of personal strength or moral guidance for its adherents.