He acted as Agent of Transports at Southampton, being appointed Resident there as from 2nd September 1796 at a salary of 21s. a day, in addition to his half-pay, and £50 a year for a clerk. This office necessitated his travelling much to the various ports, and in one of his voyages, the vessel carrying cash belonging to him was captured by the Dutch, but the Admiralty reimbursed him.

As we have seen, he was very actively superintending the arrival and distribution of prisoners of war at Hull, Yarmouth and Lynn in the early days of Norman Cross, to which Depot he was appointed Agent in 1799; he filled the post up to the Peace of Amiens, giving every satisfaction to the Admiralty and Transport Board, though on one occasion he was reprimanded for striking a French prisoner, even though the blow was given under great provocation.

His commission as Post Captain was dated 28th April 1802, and he was appointed to command the Calcutta, a ship of 74 guns to convoy convicts to Botany Bay. He was next ordered to St. Helena, to collect a convoy of East Indiamen; there were four full ships, a Prussian ship and a Swedish ship which claimed protection. They sailed on the 3rd August, and on 14th September picked up a leaky ship called The Brothers, which had become separated from another convoy. The bad condition of this vessel was the cause of all the subsequent trouble. Her bad sailing delayed the others, and off the Scilly Islands Woodriff was attacked by a French squadron of ten ships, one being a three-decker of 110 guns, with a crew of 1,100 men, four 74-gun ships, three 40-gun, and two brigs.

Finding it impossible to save both the convoy and himself, he ordered the convoy to make all sail to the north and escape, while he stayed and fought for some hours.

Over fifty minutes he was engaged with the three-decker, and the fight was under full sail as he steered to the south to enable the convoy to escape. The superior strength and overwhelming numbers of the French dismantled the Calcutta, so to prevent loss of life he hauled down his flag and surrendered, and The Brothers, which was leaky and could not escape, was also captured.

The crews were not at once landed in France, but remained on the French ships for four months. At the end of that time they were landed at Rochelle, and kept at an hotel for eighteen days at great expense. Then Captain Woodriff and his officers, an East India colonel and his lady, and two gentlemen from the East Indies, hired a carriage to take them to Verdun. They were escorted all the way by troops; the journey lasted thirty-six days and cost each of the prisoners £40.

In the Admiralty return of his services, there is a modest little note, “Returned from France, June 1807,” but the circumstances attending his return are so extraordinary as to demand attention. He had made repeated applications to Talleyrand for release, but without avail. In June 1807, he received an order, signed by Buonaparte, in Poland, directing him to proceed immediately to England, and to take the route of St. Malves, a town no Englishman was permitted to enter. On his arrival there, he received from an agent of the French Government the letters which had been directed to him at Verdun. He proceeded to hire a vessel to take him to England, for which he was prepared to pay forty or fifty guineas, but was told that a vessel was provided for him by the French Government, free of any expense whatever.

Our Government, not to be outdone in this unexpected generosity on the part of the enemy, immediately released a French officer of equal rank, who returned to France on terms of equal liberality. On his return to England Captain Woodriff was tried by court-martial for the loss of his ship the Calcutta, but after evidence, “The Court agreed that the conduct of Captain Woodriff was that of a brave, cool, and intrepid officer; and did adjudge him, his officers, and ship’s company to be most honourably acquitted.”

The owners and underwriters of one of the East Indiamen he had saved from capture raised a subscription for the officers and crew, which amounted to about £4,000.

On the 29th July 1808 Captain Woodriff was appointed Agent for Prisoners of War at Forton.