In 1886, he took part in the naval operations at Preveza as a lieutenant. During the Greco-Turkish War of 1897, serving as lieutenant commander he commanded the ship "Alfeios". His ship took part in at least two landings of Greek troops on the island of Crete. In 1901, commanding the training ship "Miaoulis", he was sent to Boston. This was reported as the first transatlantic trip of a Greek war vessel. Kountouriotis served as an aide-de-camp to King Geórgios I from 1908 until 1911, receiving the rank of Captain in 1909.