Flanagan and Allen's songs featured the same, usually gentle, humour for which the duo were known in their live performances, and during the Second World War they reflected the experiences of ordinary people during wartime. Songs like 'We're Gonna Hang out the Washing on the Siegfried Line' mocked the German defences (Siegfried Line), while others like 'Miss You' sang of missing one's sweetheart during enforced absences. Other songs, such as their most famous, 'Underneath the Arches' (which Flanagan co-wrote with Reg Connelly), had universal themes such as friendship. The music was usually melodic, following a binary verse, verse chorus structure, with a small dance band or orchestra providing the accompaniment. The vocals were distinctive because while Flanagan was at least a competent singer and sang the melody lines, Allen used an almost spoken delivery to provide the harmonies.
The recordings of Flanagan and Allen remain popular, and the duo are frequently impersonated by professionals and amateurs. Royal Variety Performances often feature people 'doing a Flanagan and Allen', notably Roy Hudd and Christopher Timothy, Bernie Winters and Leslie Crowther.
The later comedy team Morecambe and Wise, who often expressed their admiration for Flanagan and Allen, recorded a tribute album, Morecambe and Wise Sing Flanagan and Allen (Phillips 6382 095), in which they performed some of the earlier team's more popular songs in their own style, without attempting to imitate the originals. Fans of either comedy team may be slightly disappointed by this album, since all of the selections are performed absolutely straight, with no comedy except for a brief amount of banter after one of the songs.