During the final decade of his life, Cotton continued his extensive correspondence with people ranging from obscure figures to those who were highly prominent, such as Oliver Cromwell.
 His counsel was constantly requested, and Winthrop asked for his help in 1648 to rewrite the preface to the laws of New England.
 William Pynchon published a book that was considered unsound by the Massachusetts General Court, and copies were collected and burned on the Boston common.
 A letter from Cotton and four other elders attempted to moderate the harsh reaction of the court.

Religious fervor had been waning in the Massachusetts Bay Colony since the time of the first settlements, and church membership was dropping off.
 To counter this, minister Richard Mather suggested a means of allowing membership in the church without requiring a religious testimonial.
 Traditionally, parishioners had to make a confession of faith in order to have their children baptized and in order to participate in the sacrament of Holy Communion (Last Supper).
 In the face of declining church membership, Mather proposed the Half-way covenant, which was adopted.
 This policy allowed people to have their children baptized, even though they themselves did not offer a confession.

Cotton was concerned with church polity until the end of his life and continued to write about the subject in his books and correspondence.
 His final published work concerning Congregationalism was Certain Queries Tending to Accommodation, and Communion of Presbyterian & Congregational Churches completed in 1652.
 It is evident in this work that he had become more liberal towards Presbyterian church polity.
 He was, nevertheless, unhappy with the direction taken in England.
 Author Everett Emerson writes that "the course of English history was a disappointment to him, for not only did the English reject his Congregational practices developed in America, but the advocates of Congregationalism in England adopted a policy of toleration, which Cotton abhorred."

Some time in the autumn of 1652, Cotton crossed the Charles River to preach to students at Harvard.
 He became ill from the exposure, and in November he and others realized that he was dying.
 He was at the time running a sermon series on First Timothy for his Boston congregation which he was able to finish, despite becoming bed-ridden in December.
 On 2 December 1652, Amos Richardson wrote to John Winthrop, Jr.: "Mr. Cotton is very ill and it is much feared will not escape this sickness to live.
 He hath great swellings in his legs and body".
 The Boston Vital Record gives his death date as 15 December; a multitude of other sources, likely correct, give the date as 23 December 1652.
 He was buried in the King's Chapel Burying Ground in Boston and is named on a stone which also names early First Church ministers John Davenport (d. 1670), John Oxenbridge (d. 1674), and Thomas Bridge (d. 1713).
Exact burial sites and markers for many first-generation settlers in that ground were lost when Boston's first Anglican church, King's Chapel I (1686), was placed on top of them.
The present stone marker was placed by the church, but is likely a cenotaph.
During the final decade of his life, Cotton continued his extensive correspondence with people ranging from obscure figures to those who were highly prominent, such as Oliver Cromwell.  His counsel was constantly requested, and Winthrop asked for his help in 1648 to rewrite the preface to the laws of New England.  William Pynchon published a book that was considered unsound by the Massachusetts General Court, and copies were collected and burned on the Boston common.  A letter from Cotton and four other elders attempted to moderate the harsh reaction of the court.
Religious fervor had been waning in the Massachusetts Bay Colony since the time of the first settlements, and church membership was dropping off.  To counter this, minister Richard Mather suggested a means of allowing membership in the church without requiring a religious testimonial.  Traditionally, parishioners had to make a confession of faith in order to have their children baptized and in order to participate in the sacrament of Holy Communion (Last Supper).  In the face of declining church membership, Mather proposed the Half-way covenant, which was adopted.  This policy allowed people to have their children baptized, even though they themselves did not offer a confession.
Cotton was concerned with church polity until the end of his life and continued to write about the subject in his books and correspondence.  His final published work concerning Congregationalism was Certain Queries Tending to Accommodation, and Communion of Presbyterian & Congregational Churches completed in 1652.  It is evident in this work that he had become more liberal towards Presbyterian church polity.  He was, nevertheless, unhappy with the direction taken in England.  Author Everett Emerson writes that "the course of English history was a disappointment to him, for not only did the English reject his Congregational practices developed in America, but the advocates of Congregationalism in England adopted a policy of toleration, which Cotton abhorred."
Some time in the autumn of 1652, Cotton crossed the Charles River to preach to students at Harvard.  He became ill from the exposure, and in November he and others realized that he was dying.  He was at the time running a sermon series on First Timothy for his Boston congregation which he was able to finish, despite becoming bed-ridden in December.  On 2 December 1652, Amos Richardson wrote to John Winthrop, Jr.: "Mr. Cotton is very ill and it is much feared will not escape this sickness to live.  He hath great swellings in his legs and body".  The Boston Vital Record gives his death date as 15 December; a multitude of other sources, likely correct, give the date as 23 December 1652.  He was buried in the King's Chapel Burying Ground in Boston and is named on a stone which also names early First Church ministers John Davenport (d. 1670), John Oxenbridge (d. 1674), and Thomas Bridge (d. 1713). Exact burial sites and markers for many first-generation settlers in that ground were lost when Boston's first Anglican church, King's Chapel I (1686), was placed on top of them. The present stone marker was placed by the church, but is likely a cenotaph.
John Cotton (minister)