The band's fourth studio LP, Beatles for Sale, evidenced a growing conflict between the commercial pressures of the band's global success and their creative ambitions, according to Gould. They had intended the album, recorded between August and October 1964, to continue the format established by A Hard Day's Night which, unlike the band's first two LPs, contained only original songs. The band, however, had nearly exhausted their backlog of songs on the previous album, and given the challenges constant international touring posed to the band's songwriting efforts, Lennon admitted, "Material's becoming a hell of a problem". As a result, six covers from their extensive repertoire were chosen to complete the album. Released in early December, its eight original compositions stood out, demonstrating the growing maturity of the Lennon–McCartney songwriting partnership.
In early 1965, while they were his guests for dinner, Lennon and Harrison's dentist secretly added LSD to their coffee. Lennon described the experience: "It was just terrifying, but it was fantastic. I was pretty stunned for a month or two." He and Harrison subsequently became regular users of the drug, joined by Starr on at least one occasion. McCartney was initially reluctant to try it, but eventually did so in late 1966. He became the first Beatle to discuss LSD publicly, declaring in a magazine interview that "it opened my eyes" and "made me a better, more honest, more tolerant member of society."
Controversy erupted in June 1965 when Queen Elizabeth II appointed all four Beatles Members of the Order of the British Empire (MBE) after Prime Minister Harold Wilson nominated them for the award. In protest—the honour was at that time primarily bestowed upon military veterans and civic leaders—some conservative MBE recipients returned their own insignia.
Released in July, the Beatles' second film, Help!, was directed by Lester. Described as "mainly a relentless spoof of Bond", it inspired a mixed response among both reviewers and the band. McCartney said, "Help! was great but it wasn't our film—we were sort of guest stars. It was fun, but basically, as an idea for a film, it was a bit wrong." The soundtrack was dominated by Lennon, who wrote and sang lead on most of its songs, including the two singles: "Help!" and "Ticket to Ride". The accompanying album, the group's fifth studio LP, contained all original material save for two covers, "Act Naturally" and "Dizzy Miss Lizzy"; they were the last covers the band would include on an album, with the exception of Let It Be's brief rendition of the traditional Liverpool folk song "Maggie Mae". The band expanded their use of vocal overdubs on Help! and incorporated classical instruments into some arrangements, notably the string quartet on the pop ballad "Yesterday". Composed by McCartney, "Yesterday" would inspire the most recorded cover versions of any song ever written.
The group's third US tour opened with a performance before a world-record crowd of 55,600 at New York's Shea Stadium on 15 August 1965—"perhaps the most famous of all Beatles' concerts", in Lewisohn's description. A further nine successful concerts followed in other American cities. At a show in Atlanta, the Beatles gave one of the first live performances ever to make use of a foldback system of on-stage monitor speakers. Towards the end of the tour they were granted an audience with Elvis Presley, a foundational musical influence on the band, who invited them to his home in Beverly Hills.
In mid-October 1965, the Beatles entered the recording studio; for the first time in making an album, they had an extended period without other major commitments. Released in December, Rubber Soul has been hailed by critics as a major step forward in the maturity and complexity of the band's music. Their thematic reach was beginning to expand as they embraced deeper aspects of romance and philosophy. Biographers Peter Brown and Steven Gaines attribute the new musical direction to "the Beatles' now habitual use of marijuana", an assertion confirmed by the band—Lennon referred to it as "the pot album", and Starr said, "Grass was really influential in a lot of our changes, especially with the writers. And because they were writing different material, we were playing differently." After Help!'s foray into the world of classical music with flutes and strings, Harrison's introduction of a sitar on "Norwegian Wood (This Bird Has Flown)" marked a further progression outside the traditional boundaries of popular music. As their lyrics grew more artful, fans began to study them for deeper meaning. Of "Norwegian Wood" Lennon commented: "I was trying to be sophisticated in writing about an affair ... but in such a smokescreen way that you couldn't tell."
While many of Rubber Soul's more notable songs were the product of Lennon and McCartney's collaborative songwriting, it also featured distinct compositions from each, though they continued to share official credit. The song "In My Life", of which each later claimed lead authorship, is considered a highlight of the entire Lennon–McCartney catalogue. Harrison called Rubber Soul his "favorite album" and Starr referred to it as "the departure record". McCartney said, "We'd had our cute period, and now it was time to expand." However, recording engineer Norman Smith later stated that the studio sessions revealed signs of growing conflict within the group—"the clash between John and Paul was becoming obvious", he wrote, and "as far as Paul was concerned, George could do no right". In 2003, Rolling Stone ranked Rubber Soul fifth among "The 500 Greatest Albums of All Time", and Allmusic's Richie Unterberger describes it as "one of the classic folk-rock records."