It achieved its own place in pop history by being the first record to be played on Radio 1 when the station was launched in 1967 (though technically Johnny Dankworth's "Beefeaters" was the first track to be heard, since Tony Blackburn chose it as the theme tune for his Daily Disc Delivery, and so it was heard before "Flowers in the Rain"). "Flowers in the Rain" was also the last single by The Move to have Carl Wayne on lead vocals before Roy Wood took over as the band's lead vocalist for "Fire Brigade".
In a promotional stunt, for the record—typical of the band's manager Tony Secunda—a postcard was released with a cartoon of a naked Harold Wilson, linking him to his secretary Marcia Williams. Wilson sued, and the High Court ordered that all royalties from the song were donated to a charity of Wilson's choice. This legal arrangement remains in force to this day and is thought to have cost the group millions of pounds in royalties over the years. During the single's chart success, most of the money went to the Spastics Society and Stoke Mandeville Hospital. In the 1990s, The Observer newspaper reported the royalties had exceeded £200,000 and found that The Harold Wilson Charitable Trust had extended the range of beneficiaries to include, among others, the Oxford Operatic Society, Bolton Lads Club and the Jewish National Fund for Israel.
The song has been covered by Nancy Sinatra. The Kaiser Chiefs also covered this for the Radio 1 Established 1967 CD. In 1997 it was covered by Arjen Anthony Lucassen for his anonymously released album Strange Hobby.
On 25 September 2007, BBC Radio 4 featured a programme called The Story of Flowers in the Rain, hosted by Tony Blackburn, on the court action and its related history, to celebrate the 40th anniversary of the song. In the programme, the band said that although they still play the song regularly, they are beginning to get fed up with it.