Nimona offers a highly positive and inclusive portrayal of LGBTQ+ characters and themes. It features a normalized same-sex romantic relationship and a protagonist with a fluid identity, both depicted with dignity and acceptance. The film champions themes of self-acceptance and challenges societal intolerance, celebrating diverse identities.

Nimona offers a primarily allegorical and positive portrayal of trans identity through its titular character's shape-shifting, which serves as a metaphor for self-expression and gender dysphoria. The film champions individuality, self-acceptance, and the importance of being seen and understood, presenting a supportive and empowering narrative for queer themes.

The film features Nimona, a female character who repeatedly engages in direct physical combat against male guards and knights. She demonstrates clear victories by physically overpowering them using hand-to-hand combat, melee weapons, and her shapeshifting abilities.

The film allegorically portrays Christianity through the Institution, which enforces rigid, exclusionary dogma and deifies a historical figure. The narrative critiques this system as oppressive and harmful, particularly in its intolerance towards those who deviate from its norms, mirroring real-world issues of religious zealotry and anti-LGBTQ+ sentiment.