Like many other Disney theme songs, "You've Got a Friend in Me" has been covered numerous times.

Toy Story 3 also uses it for irony and dramatic effect, as the opening credits hark back to the first film and the song abruptly fades out with "And as the years go by, our friendship will never die", before showing that Andy's remaining toys in the present day are boxed up and unused.

In Toy Story 4, the song is heard during the opening montage, that features Andy playing with Woody, giving him to Bonnie as a teenager, and Bonnie playing with him, but soon starting to neglect him.

In two sequels, the song is listened to by the characters as part of the story, as cover versions done at the end of the film for thematic reasons: at the end of Toy Story 2, the character Wheezy starts to sing it to the other toys in the style of Frank Sinatra; during the end credits of Toy Story 3, Buzz Lightyear and Jessie (now a couple) perform a pasodoble to a Spanish version of the song, deliberately played by Jessie to get Buzz to dance.

The Woody's Roundup version was performed by Tom Hanks, with acoustic guitar backing; Wheezy's version was sung by Robert Goulet (though the character was voiced by Joe Ranft); and the Spanish version, "You've Got a Friend in Me (Para el Buzz Español)", was performed by the Gipsy Kings.