The arrangement, allowing two men to act simultaneously but quite independently of each other, remained in force till our own times, though its disadvantages soon began to appear. The Chaplains, though committed by their appointment to the general doctrines of the Reformation, were by no means bound to agree on the many debatable questions to which the Reformation had given rise, and did not always convey the same doctrines to their people, or work harmoniously together. It was not, however, till the year 1868 that this inconsistency was corrected by merging the two offices into one; and in 1883 the measure was supplemented by an Act which abolished the office of Chaplain altogether, and made him who then held it the first Rector.

It may here be added that the parishioners had acquired the right of appointment to the pastorate by their purchase of the church in 1614; but the scandals attending the public election at every vacancy led to its abolition in 1885, when the right was transferred to the Bishop of the diocese by Act of Parliament.[8]

In 1618 Dr. Lancelot Andrewes was appointed Bishop of Winchester, where he died in 1626. During his episcopate he often visited St. Saviour's, as the most important church in his diocese, next to his own cathedral. His pronounced churchmanship occasionally brought him into strong contrast with the Chaplains, who usually went much further in the Puritan direction than their Bishop, while they were themselves apt to be pushed forward or restrained by the parishioners. The latter, as holding the appointment in their hands, had established a sort of censorship over their pastors, which they were not slow to exercise against any tendency to "unsound" teaching. The records of the parish show that the Chaplains had to ask leave of absence when they wanted a holiday, and were otherwise kept in excellent order by their lay superiors.

About this time considerable alterations were made in the interior of the church to bring it into line with the current spiritual discipline. In or about 1615 galleries were set up for the first time across the north and south transepts, and in 1618 a screen and gallery in place of the old rood loft between the nave and choir, were "worthily contrived and erected." Somewhere between this date and 1624 an inner porch, of semi-classical design, was inserted at the west end.

That closed and rented pews were introduced at this period may be inferred from the following Representation, made by the churchwardens to the Bishop of the diocese in 1639:

"We assure your Lordship that a Pew wherein one Mrs. Ware sits, and pleads to be placed, is, and always hath been, a Pew for Women of a far better rank and quality than she, and for such whose husbands pay far greater duty than hers, and hath always been reserved for some of the chiefest Women dwelling on the Borough side of the said Parish, and never any of the Bankside were placed there, the Pews appointed for that Liberty being for the most part on the North side of the body of the Church."[9]

The Prayer-book services were suspended at St. Saviour's, as elsewhere, during the Commonwealth, by the Act of Parliament passed on 3rd January, 1645, which established the "Directory" in their place.

"The Directory for the Public Worship of God in the three Kingdoms" was not so much a book of devotions as a set of instructions to the minister, who was allowed the discretion of using what the book provided, or extemporising a service of his own upon its principles. On the Restoration of Charles II, an attempt was made at the Savoy Conference (1661) to reconcile the conflicting religious parties into which the country had been divided—an attempt which was not at all successful with those outside the Church of England. The result of the Conference, as far as the Church was concerned, was the issue of the revised Book of Common Prayer in 1662, which restored, with certain modifications, the form of services withheld during the inter-regnum.

The sacraments had been much neglected under the Protectorate; baptism was seldom administered, and the records of St. Saviour's show that marriages were then performed by the magistrates instead of the ordained ministers, the banns being published in the market-place.