1809 began with the enforced retreat of Lieutenant-General Sir John Moore's army in Spain to Corunna. Moore himself was killed defending the evacuation of his men. The year's nadir was the ill-fated Walcheren campaign, which was a military disaster. There were, however, some military successes: Martinique surrendered to Lieutenant-General Beckworth's 10,000-strong force on 24 February, St Domingo fell to Spanish and British troops in July, and Wellington had initial success on his return to Portugal, defeating the French at Talavera on 28 July. However, these successes were overshadowed by Walcheren, and the year ended with Wellington having to make a tactical withdrawal behind the defences of Torres Vedras, following the success of the French over the Austrians in the Battle of Wagram and the consequent threat of a renewed French push into Portugal. The Walcheren debacle contributed to the demise of the Portland administration, culminating in its replacement by another Tory administration led by Spencer Perceval, with Lord Liverpool becoming Secretary of State for War.

Ironically, 1809 was a good year for the Transport Board. In January Commissioner Captain James Bowen was highly praised for his strenuous efforts in managing the Corunna evacuation under extraordinarily difficult circumstances. In April a number of transports converted into fire ships were the vanguard of Captain Thomas Cochrane's success at Aix Roads; at the same time, despite the severe competition from trade, the Transport Board managed to procure a large tonnage for shipping troops returning to the Peninsula. Then in May, June and July, when trade use of merchant shipping was at an unprecedented high, the Board managed to organise the transport for 46,000 men and their equipment to Walcheren. A few months later, transports played a highly important role in the evacuation of the sick troops. The success of the Board and its agents in procuring and preparing sufficient tonnages of shipping in very difficult circumstances on these occasions demonstrated its important position in the government war machine. The significance of this was reinforced in May when Rupert George, the Chairman of the Board, was elevated to the baronetcy.