After further service in the West Indies, when he commanded the 67th Foot at San Domingo (1796–98), Stewart returned to Europe and was given permission to serve with Britain's Austrian and Russian allies in Italy, Swabia and Switzerland during the campaign of 1799.

His ideas won support, especially from the influential Equerry to the King, Colonel Coote Manningham, who Stewart had first met in the West Indies.

He devised and implemented specially adapted forms of drill and manoeuvre, medals for bravery and good conduct, classification in shooting ability, a school and a library for the soldiers, while requiring every Rifles officer to get to know each of his men as individuals.

Shortly after Stewart's twenty-seventh birthday he was appointed to command the 895 soldiers (114 from the Rifle Corps and 781 from the 49th Regiment) that were to serve as marines in the fleet sent to the Baltic in 1801.

Stewart was chosen for the honour of carrying to London the despatches reporting the victory and was included by name in the Thanks of Parliament voted on 16 April 1801.

Nelson wrote to Lord St Vincent praising "Colonel Stewart, who is an excellent and indefatigable young man, and depend upon it, the rising hope of our army".

Although Stewart was still junior as a major-general, he was given the crucial task of commanding the besieged garrison of the vital port of Cadiz and initially put directly under the orders of General Arthur Wellesley, 1st Duke of Wellington.

Suddenly attacked from flank and rear by mounted Polish lancers and French hussars, three of Colborne's regiments were massacred, losing 1,250 men; only 400 escaped.

Glover, historian of the Peninsular War, wrote, "As a battalion commander, Stewart was surpassed only by Moore; as a general he was a menace".

[4] On the opening day of the Battle of the Pyrenees at Maya Pass, Stewart concluded that the French would not attack, then rode ten miles to the rear.

for Saltash in 1795, and for Wigtonshire from 1796 onward, and on 24 June 1814 the speaker thanked him in his place, on behalf of the house, for his share in the victories of Vittoria and Orthes, and in the intermediate operations.