Nicholson was probably with the regiment when it put down Monmouth's Rebellion in 1685, but his role in some of the more unsavory behaviour on the part of Kirke's troops is unknown. 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. The dominion's governorship instead went to Sir Edmund Andros, and Nicholson, now a captain, accompanied Andros as commander of a company of infantry to Boston in October 1686. Andros sent Nicholson on what was essentially a reconnaissance mission to French Acadia. 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. Nicholson impressed Andros in this service, and was soon appointed to the dominion's council.