As at Twickenham, The Beatles performed a large variety of songs at Apple, although the original material became more focused. The sessions culminated with the famous rooftop performance on 30 January, and with a live studio set the following day for those songs which were less well suited for an outside performance.

Three of the Let It Be songs – Dig A Pony, I've Got A Feeling and One After 909 – were taken from the 30 January 1969 rooftop performance on the top of the Apple building. Dialogue from the event was also added to the end of a studio take of Get Back, with John Lennon closing The Beatles' book with the line: "I'd like to say thank you on behalf of the group and ourselves, and I hope we've passed the audition."

From the final studio session on 31 January, versions of Two Of Us and Let It Be were used on the album, and various other performances from the day were used in the film.

Glyn Johns' Get Back

Eventually, once the recording and filming was complete, The Beatles realised they had little aptitude to sift through the hours of recordings for suitable songs. That task was given to Glyn Johns, who prepared two different versions of an album, titled Get Back, both of which were rejected by The Beatles.

We let Glyn John remix it and we didn't want to know, we just left it to him and said, 'Here, do it.' It's the first time since the first album we didn't have anything to... we just said, 'Do it.' Glyn Johns did it, none of us could be bothered going in and Paul... nobody called each other about it. The tapes were left there, and we got an acetate each, and we'd call each other and say, 'Well, what do you think? Oh, let it out.' We were going to let it out with a really shitty condition, disgusted. And I wanted... I didn't care, I thought it was good to go out to show people what had happened to us. Like this is where we're at now, we couldn't get – we can't get it together and don't play together anymore. Leave us alone. Glyn Johns did a terrible job on it, 'cause he's got no idea, etc. Never mind. But he hasn't, really. And so the bootleg version is what it was like. Paul was probably thinking, 'Well, I'm not going to fucking work on it.' It was twenty-nine hours of tape, it was like a movie. I mean just so much tape. Ten, twenty takes of everything, because we're rehearsing and taking everything. Nobody could face looking at it.
John Lennon, 1970
Lennon Remembers, Jann S Wenner

Johns had been approached by Paul McCartney in December 1968 to work on the Get Back sessions. He was present throughout the sessions, and afterwards began the mammoth task of compiling an album from the tapes.

I originally put together an album of rehearsals, with chat and jokes and bits of general conversation in between the tracks, which was the way I wanted Let It Be to be – breakdowns, false starts. Really the idea was that at the time, they were viewed as being the be-all-and-end-all, sort of up on a pedestal, beyond touch, just Gods, completely Gods, and what I witnessed going on at these rehearsals was that, in fact, they were hysterically funny, but very ordinary people in many ways, and they were capable of playing as a band, which everybody was beginning to wonder about at that point, because they hadn't done so for some time – everything had been prepared in advance, everything had been overdubbed and everything, and they proved in that rehearsal that they could still sing and play at the same time, and they could make records without all those weird and wonderful sounds on them.

That became an obsession with me, and I got the bit between my teeth about it, and one night, I mixed a bunch of stuff that they didn't even know I'd recorded half the time – I just whacked the recorder on for a lot of stuff that they did, and gave them an acetate the following morning of what I'd done, as a rough idea of what an album could be like, released as it was...

They came back and said they didn't like it, or each individual bloke came in and said he didn't like it, and that was the end of that. A period of time went by and I went to America to work with Steve Miller, and when I came back, I got a call from John and Paul asking me to meet them at EMI, which I duly did. They pointed to a big pile of tapes in the corner, and said, 'Remember that idea you had about putting together an album?' and I said, 'Yes'. They said, 'Well, there are the tapes – go and do it'. So I was absolutely petrified – you can imagine. I was actually being asked to put together a Beatle album on my own. So I did – I went off and locked myself away for a week or so and pieced an album together out of these rehearsed tapes, which they then all liked, really liked. This was some months after the thing had actually been recorded, and we'd actually started work on Abbey Road about the same time.

Glyn Johns
The Record Producers

Glyn Johns began sifting through the session tapes on 10 March 1969 at Olympic Sound Studios in London. The Beatles themselves had little involvement, having begun work on Abbey Road around the same time. Johns mixed the session tapes at Olympic from 10-13 March, and on 7, 9 and 28 May. At this stage, side one of the Get Back album was to have contained One After 909, Rocker, Save The Last Dance For Me, Don't Let Me Down, Dig A Pony, I've Got A Feeling and Get Back; side two featured For You Blue, Teddy Boy, Two Of Us, Maggie Mae, Dig It, Let It Be, The Long And Winding Road and Get Back (Reprise).

For the Get Back project, it was The Beatles' intention to recreate the cover of Please Please Me, showing how thy had changed visually since 1963. In May 1969 the group returned to EMI's headquarters in London's Manchester Square, and the same photographer, Angus McBean, photographed them as they resumed their poses.

The artwork was prepared for Glyn Johns' Get Back album, which was to bear the strapline "with Let It Be and 11 other songs". For reasons unknown, however, the session photographs remained unused until the 1962-1966 and 1967-1970 (the so-called Red and Blue albums) were released in 1973.

The Beatles rejected Johns' first Get Back album, and new recording sessions for two Let It Be songs took place on 3 and 4 January 1970 – a year after the initial recordings were made.

The first of these was for George Harrison's I Me Mine, which had briefly being performed before the cameras during the 1969 sessions. In the film, Harrison first plays the song to Ringo Starr, followed by a version performed by Harrison, Paul McCartney and Starr, during which John Lennon dances with Yoko Ono.

I Me Mine, it's called. I don't care if you don't want it... It's a heavy waltz.
George Harrison
Let It Be

No proper studio recording of I Me Mine existed until 3 January 1970. It featured just Harrison, McCartney and Starr, as Lennon was on holiday in Denmark. The following day, 4 January, overdubs were recorded for Let It Be, in the band's final proper recording session together.