Robert Goodman originally pitched The Zeta Project as a darker Batman Beyond spin-off, but Kids' WB wanted shows skewing to a younger demographic and greenlit it with the reasoning 'It's a robot, and it's a teenage girl. How much fun can that be?'

The series was conceived as inspired by Frankenstein, Blade Runner, and The Fugitive, with the show's staff promising that its locations would be less dark, gothic, and oppressive than Gotham City in Batman Beyond.

Following the September 11th attacks, Kids' WB nearly cancelled the show entirely due to its terrorism plotlines and NSA commentary, though creator Bob Goodman convinced them he could continue the series without mentioning terrorists.

Character Ro Rowan was visually inspired by Pris from Blade Runner, while Agent Bennet was inspired by Lt. Philip Gerard from The Fugitive.

Agent Orin West shares a surname with and resembles Wally West, both voiced by Michael Rosenbaum, but showrunner Bob Goodman stated this resemblance was purely coincidental.

For a planned but unproduced season, Goodman intended a twist revealing that Ro was actually a robot, following a Scooby-Doo-style adventure-of-the-week format, though this idea contributed to his decision to leave the show.

After leaving the animated series, Goodman worked with actor John Schneider around 2004 on a live-action adaptation for Warner Bros. Television Studios that would have featured Ro working in the FBI's cyber crimes unit alongside a version of Zeta replacing her partner.

The Zeta Project was the final DCAU series for which composers Lolita Ritmanis, Michael McCuistion, and Kristopher Carter (the Dynamic Music Partners) used a live orchestra, an experience that helped them get hired to score Treyarch's Spider-Man video game.

Early robotic units resembling Zeta's original design, called Z-8s, later appeared in Justice League and Justice League Unlimited, and Zeta himself later appeared in the comic Batman Beyond Unlimited #16.

A tie-in browser game, Zeta Quest 3D, launched in May 2001, and its archived files include a room named 'IU8 Lab', hinting at the existence of an unproduced Infiltration Unit 8 storyline.