A pilot for the show was featured in the 1998 Channel 4 sitcom festival at Riverside Studios, but it was much darker, centering on Bernard's, and later Manny's, decision to commit suicide, and featured a character named Manny Zimmerman (a reference to Bob Dylan) and a philosophy lecturer named Valerie instead of Fran.

The series was Dylan Moran's first creation as a television writer, and the three main characters were developed over a month-long improvisational process he called 'spitballing', where he talked spontaneously in character.

Graham Linehan, co-writer of Father Ted, joined the project at the suggestion of producer William Burdett-Coutts after seeing Moran's pilot and one of his live performances in Dublin.

Moran conceived Bernard as a bookshop owner because he viewed running a second-hand bookshop as a guaranteed commercial failure, having been struck by the loneliness of real booksellers he frequented, while Linehan based Bernard's belligerent personality partly on a sign he once saw in a bookshop reading, 'Please put the books anywhere you like because we've got nothing better to do than put them back.'

The show was filmed with a multiple-camera setup, primarily at Teddington Studios in Teddington, London, with exterior scenes shot on Leigh Street and surrounding areas in Bloomsbury.

The exterior shots of the bookshop were filmed outside a real, though smaller, bookshop called Collinge & Clark at 13 Leigh Street, Bloomsbury, which stood in for the fictional address '13 Little Bevan Street'.

Black Books is considered a sister show to the 1999 Channel 4 sitcom Spaced, as both were produced by Nira Park and shared several cast members, including a scene where Manny is heard speaking to Twist Morgan, a character from Spaced.

Simon Pegg guest-starred as Bill Bailey's boss in an episode, an inversion of their character dynamic in Spaced, while Nick Frost appeared briefly to install a security system, and Kevin Cecil, one of the Black Books writers, had previously appeared in Spaced as the leader of 'Robot Club'.