On 9 March 1698 the Admiralty appointed Benbow commander-in-chief of the king's ships in the West Indies, with special orders to hunt down the pirates. His sailing was delayed until November. On the first leg of the outward passage, from Portsmouth to Madeira, Benbow provided protection against the Sale warships for the Paramore (Captain Edmond Halley), just beginning her first expedition to observe magnetic variation in the north Atlantic. Benbow did not reach Barbados until February 1699. Thence he proceeded towards the Spanish main in his flagship Gloucester (60 guns), and by a threat of blockading Cartagena induced the governor to restore two English merchant ships which he had detained to form part of a projected expedition against the Scottish colony at Darien. Benbow's action virtually put an end to this, and preserved the colonists for the time. This result seems to have been displeasing to the home government, and in June stringent orders were sent to Benbow and the governors in the West Indies 'not to assist the Scotch colony in Darien', which soon failed. The rest of the year was occupied in ineffectual efforts to persuade or constrain the Spanish commandants at Porto Bello, or Santo Domingo, to restore some ships which had been seized for illicit trading, and in a vain attempt to induce the Danish governor of St Thomas to give up some pirates who had sheltered themselves under the Danish flag. He afterwards ranged along the coast of North America as far as Newfoundland, scaring the pirates away for the time, but failing to capture any, and towards the summer of 1700 he returned to England. He was almost immediately appointed to the command in the Downs. At the time the Admiralty made this appointment, it also confirmed the commission that Benbow had given his son, John, the previous March and appointed him lieutenant in the Maidstone (24 guns). Benbow continued in the Downs through the spring and summer of 1701, operating under Admiral Sir George Rooke. In April he had been promoted to rear-admiral of the red and in July vice-admiral of the blue, flying his flag in the Breda (70 guns). In that uneasy period of peace a major concern for the English government was the Spanish silver fleet, soon expected to arrive from America. English merchants were concerned about their investments in goods valued up to 500,000 pounds, while the government feared that the French might divert the fleet and seize its cargo to support war preparations. Benbow's secret instructions authorized him to find the ships of the Spanish flota and then 'to seize and bring them to England, taking care that no embezzlement be made', even though it risked war with France and Spain. On 2 September off the Isles of Scilly, Rooke detached Benbow's squadron from the main fleet, on receiving the news that the French fleet under Chateaurenault had sailed from Brest and was apparently searching for the Spanish flota. For protection against the French squadron Benbow's ten ships were escorted on their way to the West Indies to a point beyond the usual cruising range of the French ships by the squadrons under Rear-Admiral Sir John Munden and the Dutch ships under Lieutenant-Admiral Baron van Wassenaer. Benbow's squadron arrived at Barbados on 14 November and proceeded on to Nevis and then to Jamaica, arriving in mid-December. For several months Benbow remained at Jamaica, and on 8 May 1702 he was joined by several vessels with Captain William Whetstone, who assumed the local rank of rear-admiral under Benbow. On 7 July Benbow received news that the allies had declared war on France and Spain and, within a few days, detached Whetstone with six ships to look for the French squadron under Admiral Ducasse off Port St Louis in Hispaniola, where it was anticipated he would call on his voyage en route to Cartagena. The English expected that he would make arrangements for the asiento there and prevent English and Dutch trade on that coast. Shortly after Whetstone departed Benbow and the remainder of his squadron sailed directly towards Cartagena, hoping that either his detachment or Whetstone's would encounter Ducasse. Whetstone arrived off Hispaniola after Ducasse had departed and Benbow's ships eventually sighted the French squadron on 30 August, off Cape Santa Marta. It consisted of four ships of from 68 to 70 guns, one of 40, and three transports, all under the command of Ducasse. The English force consisted of seven ships of from 50 to 70 guns, but was much scattered, and with light winds the commanders could not show great alacrity in closing. It was four in the afternoon before the ships were in any collected order, and a partial engagement, lasting a couple of hours, was ended by nightfall. Benbow had intended that the Defiance (64 guns, Captain Richard Kirkby) would lead the line of battle, but finding that Kirkby would not, or could not, maintain his station, Benbow issued a new line of battle, placing his flagship, the Breda (70 guns), in the lead. The Breda, closely followed by Captain George Walton in the Ruby (50 guns), kept company with the French all night, and was well up with them at daybreak, but the other ships did not close during the whole day. The 1st of September and three following days brought no more resolution to the different captains of the squadron. Only Walton and Captain Samuel Vincent of the Falmouth were able to support the admiral in his continued attempts to bring Ducasse to action, and for some time these three sustained the fire of the whole French squadron. The Ruby was disabled on the 3rd, and ordered to make the best of her way to Port Royal. At two in the morning the action resumed as a wind came up and all the ships were temporarily able to close the flagship from positions 2 or 3 miles astern. About three in the morning Benbow's right leg was broken by a chain-shot and he was carried below. Captain Kirkby of the Defiance came on board and urged him to give up the chase. All the other captains being summoned on board concurred, in a paper that was drafted by Kirkby and signed by all. In this they reported their views that after six days of battle the squadron lacked enough men to continue and that there was little chance of a decisive action, since the men were exhausted, there was a general lack of ammunition, the ships' rigging and masts were badly damaged, and the winds were generally variable and undependable. The captains jointly recommended to the admiral that their squadron not engage the French squadron immediately, but keep company with them throughout the night, observe them, and if wind and weather improved, try their strength once again against Ducasse. The wounded Benbow
who having seen the cowardly behaviour of some of them before, had reason to believe that they either had a design against him or to be traitors to their country if an opportunity happened that the French could have destroyed the Admiral.
ordered his squadron back to Jamaica and imprisoned the captains pending trial by court martial.
Shortly after the ships returned to Port Royal, Jamaica, Acting Rear-Admiral Whetstone also returned with his squadron, after a 62-day cruise off the coast of Hispaniola. Soon after the return to port Captain Thomas Hudson of the Pendenis died on board his ship. The remaining captains, on Benbow's orders, were remanded to the court martial board convened on board the Breda on 19-23 October 1702. Benbow delegated his normal responsibilities of presiding over the court to Whetstone, but nevertheless was present and appears to have played a dominant role in the proceedings. As a result, the court condemned captains Richard Kirkby of the Defiance and Cooper Wade of the Greenwich to be shot to death for breach of orders, neglect of duty, and for the 'ill signed paper and consultation ... which obliged the Admiral ... to give over the chase and fight'. John Constable of the Windsor was found guilty of breach of orders and drunkenness and ordered to be cashiered from the service upon return to England. The court martial board ordered Samuel Vincent of the Falmouth and Christopher Fogg of the Breda both cashiered for joining in signing the six captains' resolution, but, on Benbow's declaration that these two had fought bravely, the lord high admiral later remitted their sentence and they returned to service. Most of the court's sentences were deferred until 'her Majesty's pleasure be known therein'. After consideration in January 1703 the queen declined to hinder the sentences on Constable, Kirkby, and Wade, who were returned to England as prisoners. Constable remained imprisoned until Queen Anne pardoned him in 1704; Kirkby and Wade were shot on board the Bristol (Captain Edward Acton) in Plymouth Sound on 16 April 1703.
Meanwhile, on 15 November 1702, Benbow had died at Port Royal, Kingston.