On 23 December the British envoy, Sir William Hay Macnaghten, was murdered at Kabul; and, in February 1842, the commander-in-chief, General Elphinstone, sent orders that Kandahar was to be evacuated.

In March he inflicted a severe defeat on the enemy near Kandahar, and in May drove them with heavy loss out of the Baba Wali Pass.

In July, he received orders from Lord Ellenborough, the Governor-General of India, to evacuate Afghanistan, with permission to retire by Kabul.

On 30 August he routed the Afghans at Ghazni, and on 6 September occupied the fortress, from which he carried away, by the governor-general's express instructions, the gates of the temple of Somnath ; on the 17th he joined Pollock at Kabul.

Nott's services were highly commended; he was immediately appointed Resident at Lucknow, was presented with a Sword of Honour, and was invested as a Knights Grand Cross of the GCB.

Firstly he wed Letitia Swinhoe with whom he had five children, including Charlotte, who married John Bower and was the father of Sir William Nott-Bower.