In 1695, Coote was given commissions as governor of the English overseas possessions of New York, Massachusetts Bay, and New Hampshire, which he held until his death.

His time in New York was marked by divisive politics resulting from Leisler's Rebellion, and difficult and ultimately unsuccessful negotiations to keep the Iroquois from engaging in peace talks with New France.

Frontier issues were also at the forefront during his time in Massachusetts and New Hampshire, where lumber and security from the Abenaki threat dominated his tenure.

[5] Following the accession of the pro-Catholic James II to the English throne, Coote, a Protestant, moved to the Continent and served as a captain in a cavalry unit of the Dutch States Army.

As a result of this, William on 2 November 1689 created him Earl of Bellomont,[8] and granted him over 77,000 acres (31,000 ha) of forfeited Irish lands.

He strongly stated his view that Leisler and son-in-law Jacob Milborne had been "barbarously murdered" by Sloughter's actions in a letter to Massachusetts colonial agent Increase Mather.

Young Leisler's efforts were successful: Parliament voted to reverse the attainder, and ordered that the family properties be restored.

[13][14] The major concern that Bellomont was instructed to address was ongoing problems with piracy, including the open commerce with pirates that went on in New York City and Rhode Island.

[14] While they were being worked on, New York colonial agent Robert Livingston proposed to Bellomont that a privateer be outfitted to combat piracy, and recommended William Kidd be its captain.

[16][17] This scheme received the assent of King William, who issued a letter of marque to Kidd for the purpose, as well as a special commission for dealing with pirates.

The voyage was exceptionally stormy, and Bellomont's ship was blown well south, eventually putting into Barbados before continuing on to New York.

Bellomont's stylish dress, good looks, and positive relationship with the king predisposed New Yorkers to like him, but he very quickly ran into difficulties and began making enemies.

[21] Bellomont also approved the exhumation of the remains of Leisler and his son-in-law Jacob Milborne, which had been unceremoniously buried under the gallows from which they had been hanged.

[30] Bellomont and French Governor General Louis-Hector de Callière both claimed dominance over the Iroquois, and each refused to acknowledge the other's right to intercede on their behalf.

[32] The English emissary was unsuccessful in swaying the French from their course of action, and French-allied Algonquians made incursions deep into Iroquois territory in 1700.

[37] He also sided politically against Lieutenant Governor William Stoughton, who was an ally of Joseph Dudley, a Massachusetts native who had presided over the trial of Jacob Leisler.

Instead, he took council with the populist leader Elisha Cooke Sr.[38] Not long after his arrival in Boston, Bellomont engineered the arrest of William Kidd.

[42] Kidd then attempted to negotiate his freedom, using the secret locations of his treasure and a captured prize ship as bargaining chips.

[44] In contrast to the relative secrecy with which he conducted some of his communications with Kidd,[40] Bellomont was scrupulous in his dealings with other potentially questionable merchant and pirate business, despite being offered as much as £5,000 to overlook illicit activities.

[46] New England was recognized as an important source of ship masts for the Royal Navy, and the Board of Trade and the Admiralty sought to reserve suitable trees for the crown's benefit.

[48][50] The frontier situation that Bellomont encountered during his time in Massachusetts and New Hampshire was somewhat tense, because the Abenaki of northern New England (like the Iroquois in New York) had not been involved in the Treaty of Ryswick that ended King William's War.

[51] The Abenaki felt threatened by settler encroachment on their lands, and English colonists feared a return to significant French-inspired raiding of their settlements.

Bellomont issued proclamations to distribute among the Abenaki denying plans to take their lands, but was unable to ease the underlying tensions.

[57] Following a conference with the Iroquois at Albany in early 1700/1 (which Bellomont characterized as "greatest fatigue [I] ever underwent"), he returned to New York City,[58] where he succumbed to a severe case of gout on 5 March 1700/01.