El Chema includes LGBTQ+ characters, notably 'El Rojo,' who is openly gay and serves as a loyal associate. His sexuality is acknowledged but not central to his character's development or the main plot. The series portrays his identity incidentally, avoiding both strong affirmation and negative stereotyping. The overall depiction is neutral, as queer identity is present but neither uplifts nor denigrates within the narrative's focus on the criminal underworld.

The series frequently depicts characters who profess Christian faith, wear religious symbols, and pray to saints, yet simultaneously engage in extreme violence, drug trafficking, and other criminal acts. This creates a pervasive sense of hypocrisy, where religious practices are shown as a superficial facade or a desperate, unearned plea for divine intervention, rather than a genuine moral compass. The narrative consistently highlights this dissonance without offering significant counterbalancing positive portrayals of the faith's virtues or dignity.