Eli Stone features multiple storylines where the protagonist actively champions the legal rights of LGBTQ+ individuals. The show portrays gay couples with dignity and complexity, focusing on their universal desires for family and partnership. Obstacles are framed as external legal and societal biases, with the narrative consistently affirming the worth of LGBTQ+ lives and relationships through Eli's advocacy.

The show features a transgender character, Ethan, whose right to play on a girls' sports team is championed by the protagonist. The narrative portrays Ethan with dignity, framing societal prejudice as an external obstacle. The positive resolution affirms her identity and rights, contributing to an overall supportive portrayal.

Dr. Chen, a Buddhist acupuncturist, serves as Eli's wise spiritual mentor, offering guidance and insight into his visions. Buddhism is consistently portrayed as a source of profound wisdom, calm, and positive influence throughout the series.

The show's central premise involves a divine calling and prophetic visions, often interpreted through a Christian-adjacent spiritual lens. The narrative consistently validates Eli's spiritual journey, portraying faith and a benevolent divine influence as forces for justice and personal growth.

Judaism is portrayed positively through Rabbi George Stone, Eli's father, who is a wise, compassionate, and morally upright figure. He encourages Eli to embrace his visions as a spiritual gift, providing guidance rooted in Jewish wisdom and tradition.