In May 1810 he left service in the British Army for travel and on 26 August was well received in Ioannina by Ali Pasha, local governor for the Ottoman Empire.

Early in 1814, he returned to his seat of Cairness House until 1815 when he went abroad again to Constantinople, where he married Barbara Kana (afterwards Baroness de Sedaiges).

He refused the committee's invitation to go to Greece as one of three commissioners in charge of stores and funds stating that the Greeks were unwilling to submit to European discipline.

In 1826, renewed representations from Greece and the Greek deputies in London persuaded him to return to promote unity and military discipline.

Towards the end of June, Rumeliots forced the government to seize $10,000 from Gordon to give to the Souliot Kapetanioi from Epirus.

Having found that the Greeks besieged in the Acropolis were still able to hold out, Gordon wished to resign and only continued on condition of receiving supplies and being "entirely master of his own operations".

Nevertheless, continued resistance, the success of the Battle of Navarino, and the backing of France, the Russian Empire and the United Kingdom of Great Britain and Ireland enabled the First Hellenic Republic to emerge with a northern frontier from Arta to Volos, but without Crete or Samos.

Due to poor health, Gordon resigned his commission in February 1839 and returned to Cairness, although he made another short visit to Greece in 1840.

He had no issue with her and in his will left most of his estate, including a large landholding in Jamaica, to an illegitimate son called James Wilkinson, who later took the surname Gordon.

Gordon was awarded various honours, including being made Grand Commander of the Order of the Redeemer by the Greeks on his retirement.