Paul recorded the song on June 11th, 1968 as John worked down the hall compiling sound effects for Revolution 9. Producer George Martin was present as Paul rehearsed, but he left before proper recording began, so engineer Geoff Emerick took over the session. In his book Here, There and Everywhere, Emerick writes that Paul wanted to sound as if he were singing outdoors, so Emerick set up a stool and microphones outside behind the studio's echo chamber. The engineer actually set up three microphones - one for Paul's vocal, one for his acoustic guitar and one for his tapping foot.
Perfectionist that he is, Paul did thirty-two takes of the song, though only eleven of them were complete. Anthology 2 presents take four, which has a slightly altered structure though it is not substantially different from the master. The final take was the keeper, so it received overdubs of a second vocal during the refrains and the sound effect of a chirping bird. Emerick claims that some of the background bird sounds were picked up live by the microphones while recording.
I have in my possession a bootleg featuring Paul and Donovan chatting and trading songs, Blackbird among them. Dave Rybaczewski's in-depth article on this song says that this occurred in January of 1969 as they were getting ready to work on a session with Apple artist Mary Hopkin. Paul jokes that he had recently played the song for Diana Ross and "...she took offense - not really!" He then goes on to confirm that he had written it about the civil rights movement after hearing about some riots and demonstrates his point by emphasizing the lyrics.