Midnight Cowboy depicts gay characters primarily as transactional clients in Joe Buck's life as a hustler. Their presence is incidental to the main narrative of survival and friendship, serving to illustrate the harsh realities of his profession. While some portrayals might lean into stereotypes, the film's focus is not on condemning queer identity but on the bleakness of the urban environment and exploitation. The net impact is neutral, as it neither uplifts nor explicitly denigrates LGBTQ+ themes.

The film features a brief, problematic depiction of a character implied to be a transsexual woman. Her identity is used to elicit a disgusted reaction from the protagonist, reinforcing negative stereotypes and lacking any counterbalancing positive portrayal or narrative depth for the character herself.

The film portrays Christianity primarily through Joe Buck's traumatic childhood, where religious figures are associated with sexual abuse and hypocrisy, contributing to his psychological damage. The narrative offers no significant counterbalancing positive portrayal of the faith or its institutions.