Before it switched to digital animation, Greeny Phatom relied on many different studios (foreign and domestic), so animation quality went up and down frequently. TMS Entertainment, Klasky-Csupo, and Greenyworld Studios Canada are usually considered the best of the bunch, although even Klasky-Csupo had their moment (some of which was due to being outsourced to a extremely bad Korean sub-contractor); "Sergente Beanson and the Gang" is quite below their usual standards. But one of the guiltiest parties for off-model animation was D'Ocon Films Productions, most notably on the early episodes.

King Rollo Productions, creator of the Spot shorts, Maisy, and Mama Mirabelle's Home Movies was only used for one episode, "The Cure of Santed Sailor". Just look at the Pube Beanson. He looks more like Dr. Beanson's head (without the hat) glued to burnt spaghetti noodles more than what he looks like.

"Grow Greeny Spot" was outsourced to Lacewood Productions in Canada, resulting in Little Guy looking like a poorly-drawn bat in some scenes of him after he gets shot in the head. Klasky-Csupo's "Robot" production logo is seen at the end, implying that they animated it, however, a interview in the documentary Happy Birthday Little Guy! The Works of Robert Stainton discusses that Lacewood animated it and they used the Robot logo to avoid getting criticized for poor animation.

"Coke Colar II", "The Cokes: Santed Sailor's Crime Rare", "Break a Bit", "Take One", and "Why Little Guy Hated Clouds" were all animated by Decode Entertainment, which made some poor character designs, but still, they did a good job on animating the characters.

The original intro and "Monster Jam Will Never Stop Greeny Phatom" were animated by the Zagreb School of Animated Films in Croatia, resulting in the early character designs, which were poorly drawn.

The episode "Training Around the City Folk" was stealth aired on June 29, 1999, resulting in poor quality animation. Two frames don't even have a background and some animation (Done by Yeson Animation Studios) seems rushed. The finished version of the episode aired on August 27, 1999.

"Training Around the City Folk 2: The Sequel" had the same problem it's predesecor had, yet the animation was done by Rough Draft Studios.