Chasing Amy portrays a lesbian/bisexual character, Alyssa, primarily through the lens of male insecurity and homophobia. While Alyssa is complex, the narrative centers on the male protagonist's struggle to accept her past and features frequent homophobic remarks from a supporting character. The film's overall impact is problematic due to its focus on male discomfort with queer identity and potential reinforcement of harmful tropes.

Chasing Amy features a plot point where a main character reveals a past sexual encounter with a transsexual person. This revelation primarily serves as a source of significant discomfort and prejudice for the protagonist, Holden, leading to major conflict in his relationship. The film uses this element to highlight Holden's insecurities and inability to accept his partner's past, framing the transsexual encounter as a problematic 'baggage' rather than depicting the trans individual with dignity or agency.