American Horror Stories frequently includes LGBTQ+ characters in its anthology narratives. Their presence is integrated into the horror plots, where they experience similar fates and challenges as other characters. The show generally avoids strong positive or negative commentary on queer identity, treating it as an incidental aspect within its dark and often tragic stories.

American Horror Stories features trans characters across episodes. While one character's identity is incidental, another trans character is subjected to extreme persecution and ultimately killed by a prejudiced community, with her identity being a direct catalyst for her suffering. This results in a net negative impact due to the character's unrelieved misery and punitive outcome.

American Horror Stories frequently portrays Christian institutions and adherents in a negative light, often highlighting hypocrisy, fanaticism, and oppressive behaviors. The narrative uses Christian themes to explore dark aspects of human nature and societal failings, rather than affirming the faith.