El marginal portrays LGBTQ+ characters, notably gay men and trans women, as integral to its brutal prison world. However, their lives are overwhelmingly defined by extreme vulnerability, violence, sexual exploitation, and tragic outcomes, leading to a net negative impact despite attempts at character complexity.

El marginal features La Diosa, a transsexual inmate, portrayed with dignity, complexity, and resilience. While she faces significant prejudice and violence within the prison, these obstacles are consistently framed as external societal and systemic issues. The narrative maintains an empathetic stance, affirming her worth and agency amidst adversity, without reducing her to a stereotype.

The series portrays Christianity primarily through the lens of hypocrisy and ineffectiveness within a corrupt prison system. While a chaplain attempts to offer solace, the narrative frequently depicts inmates using religious symbols superficially while engaging in extreme violence, and the institution itself struggles to provide genuine moral guidance or positive influence.