Pink Floyd performed the piece frequently in concert from 1968 to 1973, and it became a live favourite. Concert performances gradually became significantly longer than the recorded version, often around ten minutes, and some performances feature different spoken lines by Waters.
An embryonic form was performed on 31 May 1968 at the Paradiso, Amsterdam, under the original title of "Keep Smiling People", which was filmed by NTS and broadcast on 5 July. Another version was recorded on 25 June 1968 at the BBC studio as "Mudererotic Woman" and broadcast on John Peel's Top Gear radio programme on 11 August, which Peel introduced as "Muderistic Woman". By November, it had become a regular part of the group's live show.
A version was recorded live on 2 May 1969 at the Manchester College of Commerce for the Ummagumma live album. The Ummagumma version is considerably longer than its studio counterpart and has the organ parts played on Wright's Farfisa Compact Duo rather than a Hammond. A further live version was recorded on 12 May for the BBC. For The Man and The Journey live suite, performed during mid-1969, "Careful with That Axe, Eugene" was played in the second half of the show, under the title "Beset by Creatures of the Deep". For a time, "Careful with That Axe, Eugene" was performed as the second part of a medley with "Green Is the Colour". A performance at Mont-de-l'Enclus, Belgium on 25 October 1969 was filmed and shown at select French cinemas during 1970, but not generally released. The song was played at a BBC Radio 1 concert in the BBC Paris Cinema on 16 July 1970 and at a free concert in Hyde Park two days later.
The band recorded two takes of "Careful with That Axe, Eugene" for the live film Pink Floyd: Live at Pompeii in October 1971. Contrary to the film's title, the song was recorded at Studio Europasinor, Paris. One version was used in the final film and another, titled "Careful with That Axe, Eugene (alternate version)" was released on CD as part of the Early Years box set. Both versions run for under seven minutes.
Footage also exists of the group performing the piece on the Australian TV programme GTK, filmed on 15 August 1971 at Randwick Racecourse, Sydney. It was broadcast with the live version from Ummagumma dubbed onto the footage. The performance at the Brighton Dome on 29 June 1972 was filmed by Peter Clifton for the film Sounds of the City 1964–1973. It was one of four Pink Floyd songs that the group played while accompanied with ballet choreographed by Roland Petit. The concerts ran in November 1972 at the Salle Valliers, Marseille, followed by a series of concerts at the Palais de Sports, Paris, in January and February 1973.