When the German Army invaded France in May 1940, the 2nd, 5th and 1/9th Manchesters formed part of the British Expeditionary Force - the 2nd and 1/9th were Machine Gun battalions.The 2nd Battalion, a Regular Army unit, was the MG Battalion of the 2nd Infantry Division, the 5th was serving with 4th East Lancashire Regiment and 1st Highland Light Infantry in the 127th Infantry Brigade, 42nd (East Lancashire) Infantry Division and the 1/9th was with III Corps GHQ Troops. Despite putting up a stubborn defence, the BEF went into retreat, the Manchesters being engaged along the way. Much of the BEF converged on Dunkirk, where hundreds of ships evacuated more than 330,000 soldiers back to Britain. Of the surviving men of the 2nd Manchesters, more than 300 men were evacuated. Fewer than 200 remained, fighting until being either captured or killed. The 5th and 1/9th were also evacuated, having suffered light casualties. The evacuation ended on 3 June. Captain Jack Churchill, the only known man to kill an enemy with a longbow in the Second World War, was serving with the Manchester Regiment during this period.
In November 1941, the 5th Manchesters, along with the rest of the division (which became 42nd Armoured Division), was converted to armour as the 111th Regiment Royal Armoured Corps (Manchester Regiment), serving alongside the 107th Regiment Royal Armoured Corps (King's Own) and the 110th Regiment Royal Armoured Corps (Border) in the 11th Armoured Brigade. The men continued to wear their Manchester Regiment cap badge on the black beret of the RAC as did all infantry units converted in this way. However, 111 RAC was disbanded in November 1943 and 5th Manchesters reconstituted as an infantry battalion. In the summer of 1944, the battalion acted as the Royal Bodyguard at Balmoral Castle while the Royal Family was in residence and then served as a machine-gun battalion with 55th (West Lancashire) Infantry Division until the end of the war.[
In November 1941, the 2/9th Manchesters, a 2nd Line Territorial Army duplicate of the 1/9th and a Machine Gun Battalion, was transferred to the Royal Artillery and converted into the 88th Anti-Tank Regiment, Royal Artillery. (Sometime after this, the 1/9th Battalion was redesignated as the 9th Battalion.) The 88th Anti-Tank Regiment was part of the 49th (West Riding) Infantry Division until July 1943 when it transferred elsewhere and, in January 1944, the regiment was transferred to 45th (Holding) Division where it converted to the 88th Training Regiment, Royal Artillery.