A series of illnesses and deaths in Anson's squadron meant that by early 1741 Murray had been promoted to post captain and given command of the frigate HMS Pearl.

Pearl and another ship lost contact with Anson in April of that year and after taking heavy damage and casualties through storms and sickness, sought safety in Rio de Janeiro before sailing for England.

Murray continued in the navy after this, receiving a number of different commands including the ship of the line HMS Hampshire in which he served in the Mediterranean Sea and English Channel.

[2][3][4] On 1 August he was appointed second lieutenant of the frigate HMS Ludlow Castle on board which he served for over a year completing "secret service" duties, leaving on 13 September 1729 when she was paid off.

[8][3] On 9 December 1737 Murray became second lieutenant of the ship of the line HMS Hampton Court which sailed for the West Indies in 1738 as the flagship of Commodore Charles Brown.

[3][12] Murray and Hampshire served in a squadron stationed off Cape Ortegal and there he captured the Spanish privateer Nuestra Senora del Rosario on 22 December before transferring to Norris' fleet in the Channel in 1744.

[18][3] He then recommissioned the ship of the line HMS Duke on 23 September 1755, but this command came to an end on 15 June 1756 when Murray chose to retire from active service in the navy.