"Prototype" received critical acclaim, predominantly directed towards its instrumentation and sonic quality, both upon the release of Speakerboxxx/The Love Below and in retrospective commentaries.

The song's accompanying music video, directed by André 3000 himself, depicts him as an interstellar traveler who lands on Earth and falls in love with a woman.

To promote the song, Outkast performed it live at the 2004 MTV Video Music Awards, subsequently including it on the set list for their 2014 reunion tour.

Following the end of promotional activities in support of their widely successful fourth studio album Stankonia (2000), Outkast embarked on a brief hiatus.

Feeling discontented with hip hop, he started writing pop, funk and jazz-oriented songs incorporating singing and playing instruments, with a restrict on rapping.

[6] Multiple journalists defined it as a funk track,[6][7] while Jon O'Brien from The Recording Academy described its musical style as "celestial neo soul".

[13] In Stylus Magazine, Nick Southall wrote the track was one of "the best things Outkast have ever recorded", describing it as "blissful Prince slink".

[15] Stereo Williams from The Daily Beast described it as "a lilting ballad featuring 3000 cooing uncertain and lovelorn lyrics over smooth guitar lines".

[16] The Ringer included the track on their listing of Outkast's best songs, calling it "a transportive jaunt that feels more than it sounds", commending its lyrical content and integration of funk and hip hop styles.

[17] The accompanying music video for "Prototype", an homage to Sun Ra's movie Space Is the Place,[18] marked André 3000's directorial debut and was filmed during the weekend of July 30–August 1, 2004.

[17] It depicts him as a member of an extraterrestrial family, all wearing white wigs and futuristic clothing, descending to Earth from a fictional planet Proto and landing in an "idyllic" rural area.