With Pasley he afterwards served in the Jupiter, in the squadron under Commodore George Johnstone, and was present at the action in Porto Praya and at the capture of the Dutch Indiamen in Saldanha Bay.

He continued serving during the peace, and in 1793, at the beginning of the French Revolutionary Wars, was first lieutenant of the Penelope frigate on the Jamaica station, under the command of Captain Bartholomew Rowley.

After some further cruising among the islands the Fox returned to India, where, on 18 June, Malcolm was appointed by Rear-Admiral Rainier to be his flag captain in the Suffolk, and afterwards in the Victorious.

On her homeward passage, in 1803, the Victorious proved exceedingly leaky, and, meeting with heavy weather in the North Atlantic, was with difficulty kept afloat till she reached the Tagus, where she was run ashore and broken up.

It was not till the beginning of 1805 that he was permitted to rejoin the flag, and to exchange into the Donegal, in time to take part in the celebrated pursuit of the French fleet to the West Indies (see Horatio Nelson).

"[2] The Donegal continued off to cruise off Cadiz till the close of the year, when she sailed for the West Indies with Sir John Duckworth, and took an important part in the Battle of San Domingo, 6 February 1806.

In 1808 he was engaged in convoying troops to the Peninsula, and in 1809, still in the Donegal, was attached to the Channel Fleet, then commanded by Lord Gambier, and took part in the Battle of the Basque Roads.

The Donegal was paid off in 1811, and Malcolm was appointed to the Royal Oak, which he commanded off Cherbourg till March 1812, when he accepted the post of captain of the fleet to Lord Keith, his uncle by marriage.

On 2 January 1815 he was nominated a K.C.B., and during "The Hundred Days' War" commanded a squadron in the North Sea, in co-operation with the army under the Duke of Wellington.

In 1816–17 he was Commander-in-chief on the Saint Helena station, specially appointed to enforce a rigid blockade of the island and to keep a close guard on Napoleon Bonaparte.

In the final years of his life, he became Chairman of the Oriental Club[5] which had been founded by his brother General Sir John Malcolm.