Salisbury
Wheelwright's position at the church in Hampton had, as expected, been filled during his absence, but he was quickly called by residents of the neighboring town of Salisbury to be their pastor, and on 9 December 1662, when 70 years old, he was installed there. This became Wheelwright's longest pastorate in his varied life, lasting nearly 17 years. Probably the most noteworthy event of his tenure in Salisbury occurred very late in his life when Major Robert Pike, a layman and very prominent member of his church, collided with him during the winter of 1675 to 1676. There may have been multiple reasons for the severe friction between the men, one of them being that Wheelwright was against the Quaker insurgence into New England, whereas Pike was much more tolerant of their evangelism. Another reason may have been that during the election of 1637, Pike traveled all the way from Newbury to Newtown to vote Governor Vane out of office. A more recent and local cause of dissension was likely over the division of Salisbury when the town of Amesbury was created from it several years earlier. Pike had made certain claims of Wheelwright, to which Wheelwright wrote a petition to the court, and on 10 March 1676 the court sided with Wheelwright. Not easily rebuked, Pike enlisted support from other members of the church and town, following which Wheelwright called for intervention by civil authorities.
The intervention did not occur immediately, leaving the two sides to cast aspersions at each other. While a majority of church members supported Wheelwright, a large minority were in support of Pike, and when the brethren attempted to subject Pike to discipline for misconduct, he contemptuously refused the judgment, and Wheelwright then excommunicated him from the church. In the spring of 1677 several disaffected members of the church and town petitioned the court that Wheelwright was the cause of the disturbance, and that his preaching had a tendency to pit one person against another, and requested he be removed from the ministry. Pike's biographer wrote in 1879 that Pike "opposed Wheelwright, and the arbitrary devices of his church polity, to the extent of incurring excommunication." The legislature appointed a committee, earlier proposed by Wheelwright, and through much effort was able to establish a peace. Both parties were assigned fault in the matter, Pike was required to make a concession of his faults, and the church was prompted to return him to communion. From all that is known, the matter was resolved, and did not recur.
In October 1677, Wheelwright sold his property in Lincolnshire, (purchased of Francis Levett, gentleman) to his son-in-law Richard Crispe, the husband of his youngest daughter, Sarah. In June 1679, Wheelwright was given, following a much earlier recommendation, an assistant, the Reverend George Burroughs, who later became the only minister executed during the Salem witch trials.
At nearly 87 years old, Wheelwright died of apoplexy on 15 November 1679 and was buried at the East Village Graveyard, where no marker had been placed for the next 200 years. The graveyard became the Colonial Burying Ground of Salisbury, and memorials have since been installed recognizing Wheelwright's historical significance.
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