Nicholson's military service included time in Africa and Europe, after which he was sent to North America as leader of the troops supporting Governor, Sir Edmund Andros in the Dominion of New England.

After news of the Glorious Revolution and the overthrow of King James II reached the colonies in 1689, Andros was himself overthrown in the Boston Revolt.

During the service in Tangier he met a number of people who would figure prominently North American colonial history, including Thomas Dongan and Alexander Spotswood.

[6] Kirke, who had been selected by Charles II as the governor of the prospective Dominion of New England, was strongly criticized for his role in the quashing of the rebellion, and James withdrew his nomination.

Under the cover of delivering a letter protesting a variety of issues to the Acadian governor, Nicholson made careful observations of Port Royal's defenses.

[8] Nicholson's rule, in which he was assisted by a local council but no legislative assembly, was seen by many New Yorkers as the next in a line of royal governors who "had in a most arbitrary way subverted our ancient privileges".

However, the province's old guard was unhappy that Andros removed all of the provincial records to Boston, and then Nicholson alarmed the sometimes hardline Protestant population by preserving the trappings of the chapel in Fort James that Dongan and the handful of New York's Catholics had used for worship.

[13] After James was deposed by William III and Mary II in the Glorious Revolution in late 1688, Massachusetts rose up in rebellion against Andros, arresting him and other dominion leaders in Boston.

[16] When word of the Boston revolt reached Long Island, politicians and militia leaders became more assertive, and by mid-May dominion officials had been ousted from a number of communities.

[17] At the same time, Nicholson learned that France had declared war on England, bringing the threat of French and Indian attacks on New York's northern frontier.

[15] In an attempt to mollify panicked citizenry over rumored Indian raids, Nicholson invited the militia to join the army garrison at Fort James.

Leisler was a vocal opponent of the dominion regime, which he saw as an attempt to impose "popery" on the province, and may have played a role in subverting Nicholson's regulars.

[19] On 22 May Nicholson's council was petitioned by the militia, who, in addition to seeking more rapid improvement to the city's defenses, also wanted access to the powder magazine in the fort.

[28] Despite the efforts of Charles Paulet (now Duke of Bolton) and other patrons, William in November instead chose Colonel Henry Sloughter to be the next governor of New York.

[35] When Nicholson, now appointed governor of Maryland, arrived in July, he found the provincial treasury empty, and testily demanded that Andros return the payment.

[38] Nicholson, a committed Anglican as a member of the Church of England, sought to reduce Roman Catholic influence in the Maryland government, and moved the old colonial capital from the Catholic stronghold of St. Mary's City in southern Maryland's St. Mary's County along the Potomac River to what was then called "Anne Arundel's Town" (also known briefly as "Providence"), which was later renamed "Annapolis" in honour of the future monarch, Princess Anne.

He chose its site and laid out the plan for the town, placing the Anglican (later Episcopal church and the state house in well-designed public spaces (known later as "State Circle" and "Church Circle") and the use of diagonal avenues to connect various parts of the town (foreseeing details of Pierre L'Enfant's, (1754–1825), plan for the National Capital or "Federal City" in Washington and the District of Columbia, a century later.

Architectural historian Mark Childs describes Annapolis, along with Williamsburg, Virginia, which Nicholson also laid out during his later tenure there, as some of the best-designed towns in the British Empire.

[46] Nicholson made a number of unsuccessful attempts to alter the balance of power, including moving the provincial capital from Jamestown to Middle Plantation, which was renamed Williamsburg.

He warned the Board of Trade in 1695 that the French were working to complete the designs of explorer Robert La Salle to gain control of the river and dominate the Indian relations in the interior, which "may be of fatal consequence" to the English colonies.

[49] He actively promoted the idea of expansionist trade on the frontier with other colonial governors, including Bellomont of New York, and Blake of South Carolina.

[50] Following a political crisis in England and the accession of Queen Anne to the throne in 1702, a Tory ministry emerged that sidelined most of Nicholson's Whig patrons.

[52] During King William's War in the 1690s Nicholson asked the House of Burgesses to appropriate money for New York's defense, since it was threatened from New France and acted as a buffer to protect Virginia.

Nicholson was able to draw on his earlier connections to New York's aristocracy to recruit the needed forces from there, with additional units coming from New Jersey and Connecticut.

[61] He raised a force of about 1,500 regulars and provincial militia and 600 Iroquois, and in June began the construction of three major encampments between Stillwater, just north of Albany, and the southern end of Lake Champlain, while awaiting word of the fleet's arrival in Boston.

[62] In the aftermath of the debacle Nicholson returned to London, taking four Indian chiefs with him, and petitioned Queen Anne for permission to lead a more limited expedition against Port Royal, the capital of French Acadia.

Many ships of Walker's fleet foundered on rocks near the mouth of the Saint Lawrence River, and the whole expedition was cancelled, much to Nicholson's anger;[2] he was reported to tear off his wig and throw it to the ground when he heard the news.

[67] Vetch and the Tory ministry then in power disagreed on how to handle affairs, especially with respect to the resident French Catholic population,[68] and Nicholson capitalized on these complaints.

Nicholson also issued order restricting the interaction between the troops and the town, resulting in the further reduction of already-poor morale in the Port Royal garrison.

Combined with long-running but false accusations by William Rhett and other supporters of the proprietors that Nicholson was improperly engaged in smuggling, he felt the need to return to England to defend himself against these charges.