In the summer of 1809 he sailed with the expedition sent to occupy the French-occupied Ionian Islands. Here he increased the reputation he had already gained by forming a Greek regiment in British pay. On 9 September 1809 he took the position of Major in the 1st Regiment Greek Light Infantry. On 19 November 1812 he became Lieutenant-Colonel of the unit, by then renamed The Duke of York's Greek Light Infantry Regiment (1811 – 24 February 1816). Having got the experience of managing foreign troops, he commanded the regiments made up from Greeks he recruited himself in 1813, when he formed a second regiment composed of 454 Greeks (2nd Regiment Greek Light Infantry) to occupy Paxoi islands. These regiments included many of the men who were afterwards among the leaders of the Greeks in the War of Independence including Theodoros Kolokotronis, with whom he kept a friendship and correspondence. Church commanded this regiment at the taking of the island of Santa Maura (Lefkada), on which occasion his left arm was shattered by a bullet.