Miller was commissioned lieutenant on 18 March 1783 and placed in command of the armed schooner Gros Inlet by Admiral Hugh Pigot, the commander-in-chief of the Leeward Islands station. He was promoted commander of the same vessel just four days later on 22 March, and he appears to have retained her until the last week of May.
On 2 November 1790 he was appointed to the storeship Camel 44, which was put into commission at Woolwich, and he retained her until the end of March 1791.
On 18 January 1793, just prior to the commencement of the French Revolutionary War, Miller accepted the command of the Experiment 44 en-flute, which on 26 February departed from St. Helens under the orders of Captain Samuel Osborn of the Centurion 50 with artillerymen for Gibraltar. Sailing thereafter for the Leeward Islands, it was reported that the Experiment suffered so badly from yellow fever towards the end of the year that at one point she only had eleven fit crew members, and it is probable that Miller was indisposed during this period and temporarily relinquished command.
He participated in the Leeward Islands campaign which commenced under Vice-Admiral Sir John Jervis in January 1794, and he was posted captain of the Vanguard 74 on 4 November, flying the flag of Rear-Admiral Charles Thompson. During April 1795 the Vanguard escorted the outward-bound Portsmouth convoy from Martinique to Antigua, and after conducting the homeward-bound convoy into the Atlantic she captured the French corvette Perdrix 20 near the Bermudas on 15 June, which prize was sent into Antigua. Following Thompson’ return home in August she continued as a private vessel, and to the west of Deseada on 30 September she took the Superbe 22 en-flute, which was sailing for Guadeloupe with dispatches. She also captured a vessel under Danish colours which was carrying a French commissioner out to the latter countries’ possessions.
Towards the end of 1796 it was reported that the Vanguard had lost a huge number of her crew to yellow fever at St. Lucia, and had been re-manned by men from the Port Royal guardship Scipio 64. She eventually came home with a convoy in the summer of 1797, and after arriving at Chatham on 27 July she was paid off in August. During his long service in the West Indies Miller had survived three bouts of yellow fever.
He does not appear to have seen any further service and was superannuated as a rear-admiral on 16 August 1814.
Admiral Miller he died at Mitcham, Surrey in May 1825, and he was buried next to his wife at Twyford near Winchester. where the couple had lived in retirement.
On 30 June 1785 he married Elizabeth Todd of Greenwich at Bexley St. Mary in Kent, and after her death near Blackheath in early 1799 he appears to have remarried, for it was reported that his wife had died on 31 March 1823 aged 67.