The show features multiple openly LGBTQ+ main characters whose identities are integrated into the narrative. While their sexualities are frequently the subject of the show's characteristic dark and often problematic humor, these characters are also depicted with agency, competence, and complexity. This prevents their identities from being solely a source of ridicule or misery, balancing problematic jokes with character depth for a neutral net impact.

Archer features a storyline where character Ray Gillette undergoes a temporary 'sex change' for a spy mission. This plot point, where Ray becomes 'Rayette' and later reverts, is primarily played for comedic effect. The portrayal treats gender transition as a superficial, reversible procedure, rather than exploring gender identity with dignity or empathy, thus contributing to potentially harmful stereotypes.

The show features multiple female characters who are highly skilled in physical combat. Lana Kane and Pam Poovey frequently engage in and win hand-to-hand fights against one or more male opponents, demonstrating superior strength and martial arts proficiency.

The show frequently satirizes Christian institutions and figures, often portraying them as corrupt, hypocritical, or foolish, particularly through characters whose religious references are self-serving. The narrative uses Christian elements for comedic effect or to highlight human flaws, rather than affirming the faith's virtues or condemning bigotry against it.