- The 3D version has many changes to make use of the process:
- Fireflies were added to the "Where to Begin..." shot, along with the removal of a flare.
- The "Walt Disney Pictures presents" now has a sky background, and both texts have a drop shadow effect while the top slowly zooms in.
- A bench was removed when the water tower ball crushed the movie theater.
- Two extra balls were added during the "Gonna Make You Sweat (Everybody Dance Now)" song.
- An extra plane was added when Fish Out of Water was re-enacting King Kong.
- Extra dirt was added when the cow fell to the centerfield.
- When Chicken Little tries to point at the piece of sky, he now points at the camera instead of the left.
- When we first see the aliens, their grappling hooks are now moved to the center of the screen.
- When the aliens switched from their grappling hooks to their knives, the front was rotated so it could look at the camera.
- Both camera and alien overlays were now stretched to fit the entire image.
- One of the shots to when the aliens start cracking parts of the fake sky to start their invasion was re-animated, and a bunch of debris was added falling in.
- Electric sparks were added when the motherships separated. This could possibly have originally been a goof in the 2D version since the sounds of it were left intact.
- Extra magic dust was added after the characters sing "Don't Go Breaking My Heart," and the credits appear a second early.
- Credits for the 3D conversion were added, extending the credits to when the music ends.
- The Disney logo was replaced with a specially made post-credits scene featuring Buck Cluck saying goodbye to the audience and Chicken Little asking if they can have some popcorn once they leave, to which his father replied that there is some on the floor.
- International theatrical prints of the film completely remove the "one year later" and alien subtitles, so a translation can be added by the editor. Also, the last part of the end credits was in a slideshow format, which Disney would later use again in Meet the Robinsons (2007).
- On Australian theatrical prints of the film, Mark Mitchell provided the voice of Buck Cluck. Despite not being included on all Australian home media releases, it would later be included as a bonus audio option when it was streamed on Disney+.
- The Spanish dubs of the film features the song "Todos Tenemos A Alguien", performed by Alejandro Lerner, during the end credits.
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