Seed of Chucky explores gender identity through Glen/Glenda's journey of self-discovery. While Chucky's reactions are prejudiced, Tiffany's acceptance provides a counterpoint. The film ultimately allows both aspects of Glen/Glenda's identity to be realized and thrive, framing external obstacles while affirming their self-determination.

Seed of Chucky features Glen/Glenda, a character exploring gender identity. The film portrays a supportive parent (Tiffany) who affirms Glenda's identity against the transphobic views of Chucky, the villain. Despite its comedic horror tone, the narrative ultimately allows for the expression and affirmation of Glen/Glenda's gender identities, leading to a net positive portrayal.

The film uses Christian themes and characters, such as the devout Joan, for dark comedic effect and to highlight their naivete. It often portrays faith as easily exploited or as a backdrop for the dolls' blasphemous actions, without offering any affirming or nuanced perspective.