The season was to end prematurely, with competitive football abandoned with the outbreak of World War II.

After only three Southern League games, World War II was declared, and as with predecessors Colchester Town during World War I, the club closed down, denying the club a chance to earn League football after gaining considerable momentum over the previous two seasons.

Colchester United continued to play friendlies against local opposition until December 1939, when the Army Fire Fighting Corp took over Layer Road for drill practice.

The ground itself did continued to host matches during hostilities, as a number of high-profile military encounters took place at the stadium.

The influx of military personnel through Colchester Garrison ensured that Layer Road played host to a number of star players through the war years.