The Savoy Declaration substitutes the following for Chapter 23 § 3 of the Westminster Confession.

Although the magistrate is bound to encourage, promote, and protect the professors and profession of the gospel, and to manage and order civil administrations in a due subserviency to the interests of Christ in the world, and to that end to take care that men of corrupt minds and conversations do not licentiously publish and divulge blasphemy and errors, in their own nature subverting the faith and inevitably destroying the souls of them that receive them; yet in such differences about the doctrines of the gospel, or ways of the worship of God, as may befall men exercising a good conscience, manifesting it in their conversation, and holding the foundation, not disturbing others in their ways or worship that differ from them, there is no warrant for the magistrate under the gospel to abridge them of their liberty.

The following chapter is added to the Confession as Chapter 20.

Chapter 20.
Of the Gospel, and of the Extent of the Grace Thereof.

1. The covenant of works being broken by sin, and made unprofitable unto life, God was pleased to give unto the elect the promise of Christ, the seed of the woman, as the means of calling them, and begetting in them faith and repentance. In this promise the gospel, as to the substance of it, was revealed, and was therein effectual for the conversion and salvation of sinners.

2. This promise of Christ, and salvation by him, is revealed only in and by the Word of God; neither do the works of creation or providence, with the light of nature, make discovery of Christ, or of grace by him, so much as in a general or obscure way; much less that men, destitute of the revelation of him by the promise or gospel, should be enabled thereby to attain saving faith or repentance.

3. The revelation of the gospel unto sinners, made in divers times and by sundry parts, with the addition of promises and precepts for the obedience required therein, as to the nations and persons to whom it is granted, is merely of the sovereign will and good pleasure of God, not being annexed by virtue of any promise to the due improvement of men's natural abilities, by virtue of common light received without it, which none ever did make, or can so do: and therefore in all ages the preaching the gospel hath been granted unto persons and nations, as to the extent or straitening of it, in great variety, according to the counsel of the will of God.

4. Although the gospel be the only outward means of revealing Christ and saving grace, and is as such abundantly sufficient thereunto; yet that men who are dead in trespasses may be born again, quickened, or regenerated, there is moreover necessary an effectual, irresistible work of the Holy Ghost upon the whole soul, for the producing in them of a new spiritual life, without which no other means are sufficient for their conversion unto God.

The Savoy Declaration ends with the following platform of Congregational church order, which serves as a replacement for Chapters 30 and 31 of the Westminster Confession.

Of the Institution of Churches, and the Order Appointed in Them by Jesus Christ.

1. By the appointment of the Father, all power for the calling, institution, order, or government of the Church is invested in a supreme and sovereign manner in the Lord Jesus Christ, as King and Head thereof.

2. In the execution of this power wherewith he is so entrusted, the Lord Jesus calleth out of the world unto communion with himself those that are given unto him by his Father, that they may walk before him in all the ways of obedience which he prescribed to them in his Word.

3. Those thus called (through the ministry of the Word by his Spirit) he commandeth to walk together in particular societies or churches, for their mutual edification, and the due performance of that public worship which he requireth of them in this world.

4. To each of these churches thus gathered, according unto his mind declared in his Word, he hath given all that power and authority which is any way needful for their carrying on that order in worship and discipline which he hath instituted for them to observe, with commands and rules for the due and right exerting and executing of that power.

5. These particular churches thus appointed by the authority of Christ, and entrusted with power from him for the ends before expressed, are each of them as unto those ends the seat of that power which he is pleased to communicate to his saints or subjects in this world, so that as such they receive it immediately from himself.

6. Besides these particular churches, there is not instituted by Christ any Church more extensive or catholic entrusted with power for the administration of his ordinances or the execution of any authority in his name.

7. A particular church gathered and completed according to the mind of Christ consists of officers and members, the Lord Christ having given to his called ones (united according to his appointment in church order) liberty and power to choose persons fitted by the Holy Ghost for that purpose, to be over them and to minister to them in the Lord.

8. The members of these churches are saints by calling, visibly manifesting and evidencing (in and by their profession and walking) their obedience unto that call of Christ, who being further known to each other by their confession of the faith wrought in them by the power of God, declared by themselves, or otherwise manifested, do willingly consent to walk together according to the appointment of Christ, giving up themselves to the Lord and to one another by the will of God, in professed subjection to the ordinances of the gospel.

9. The officers appointed by Christ to be chosen and set apart by the church so called, and gathered for the peculiar administration of ordinances and execution of power or duty which he entrusts them with, or calls them to, to be continued to the end of the world, are Pastors, Teachers, Elders, and Deacons.

10. Churches thus gathered and assembling for the worship of God are thereby visible and public, and their assemblies (in what place soever they are, according as they have liberty or opportunity) are therefore church or public assemblies.

11. The way appointed by Christ for the calling of any person, fitted and gifted by the Holy Ghost, unto the office of Pastor, Teacher, or Elder, in a church, is that he be chosen thereunto by the common suffrage of the church itself, and solemnly set apart by fasting and prayer, with imposition of hands of the Eldership of that church, if there be any before constituted therein; and of a Deacon, that he be chosen by the like suffrage, and set apart by prayer and the like imposition of hands.

12. The essence of this call of a Pastor, Teacher, or Elder unto office consists in the election of the church, together with his acceptation of it, and separation by fasting and prayer; and those who are so chosen, though not set apart by imposition of hands, are rightly constituted ministers of Jesus Christ, in whose name and authority they exercise the ministry to them so committed. The calling of Deacons consisteth in the like election and acceptation, with separation by prayer.

13. Although it be incumbent on the Pastors and Teachers of the churches to be instant in preaching the Word, by way of office, yet the work of preaching the Word is not so peculiarly confined to them but that others also gifted and fitted by the Holy Ghost for it, and approved (being by lawful ways and means in the providence of God called thereunto), may publicly, ordinarily, and constantly perform it, so that they give themselves up thereunto.

14. However, they who are engaged in the work of public preaching, and enjoy the public maintenance upon that account, are not thereby obliged to dispense the seals to any other than such as (being saints by calling, and gathered according to the order of the gospel) they stand related to as Pastors or Teachers; yet ought they not to neglect others living within their parochial bounds, but besides their constant public preaching to them, they ought to inquire after their profiting by the Word, instructing them in and pressing upon them (whether young or old) the great doctrines of the gospel, even personally and particularly, so far as their strength and time will admit.

15. Ordination alone, without the election or precedent consent of the church, by those who formerly have been ordained, by virtue of that power they have received by their ordination, doth not constitute any person a church officer, or communicate office-power unto him.

16. A church furnished with officers according to the mind of Christ hath full power to administer all his ordinances; and where there is want of any one or more officers required, that officer, or those which are in the church, may administer all the ordinances proper to their particular duty and offices; but where there are no teaching officers, none may administer the seals, nor can the church authorize any so to do.

17. In the carrying on of church administrations, no person ought to be added to the church but by the consent of the church itself; that so love (without dissimulation) may be preserved between all the members thereof.

18. Whereas the Lord Jesus Christ hath appointed and instituted, as a means of edification, that those who walk not according to the rules and laws appointed by him (in respect of faith and life, so that just offense doth arise to the church thereby) be censured in his name and authority: Every church hath power in itself to exercise and execute all those censures appointed by him, in the way and order prescribed in the gospel.

19. The censures so appointed by Christ are Admonition and Excommunication; and whereas some offenses are or may be known only to some, it is appointed by Christ that those to whom they are so known do first admonish the offender in private (in public offenses where any sin, before all), and in case of non-amendment upon private admonition, the offense being related to the church, and the offender not manifesting his repentance, he is to be duly admonished in the name of Christ by the whole church, by the ministry of the Elders of the church; and if this censure prevail not for his repentance, then he is to be cast out by Excommunication, with the consent of the church.

20. As all believers are bound to join themselves to particular churches, when and where they have opportunity so to do, so none are to be admitted unto the privileges of the churches who do not submit themselves to the rule of Christ in the censures for the government of them.

21. This being the way prescribed by Christ in case of offense, no church members, upon any offenses taken by them, having performed their duty required of them in this matter, ought to disturb any church order, or absent themselves from the public assemblies or the administration of any ordinances, upon that pretense, but to wait upon Christ in the further proceeding of the church.

22. The power of censures being seated by Christ in a particular church, is to be exercised only towards particular members of each church respectively as such; and there is no power given by him unto any synods or ecclesiastical assemblies to excommunicate, or by their public edicts to threaten Excommunication or other church censures against churches, magistrates, or their people, upon any account, no man being obnoxious to that censure but upon his personal miscarriage as a member of a particular church.

23. Although the church is a society of men assembling for the celebration of the ordinances according to the appointment of Christ, yet every society assembling for that end or purpose, upon the account of cohabitation within any civil precincts or bounds, is not thereby constituted a church, seeing there may be wanting among them what is essentially required thereunto; and therefore a believer living with others in such a precinct may join himself with any church for his edification.

24. For the avoiding of differences that may otherwise arise, for the greater solemnity in the celebration of the ordinances of Christ, and the opening a way for the larger usefulness of the gifts and graces of the Holy Ghost, saints living in one city or town, or within such distances as that they may conveniently assemble for divine worship, ought rather to join in one church for their mutual strengthening and edification than to set up many distinct societies.

25. As all churches and all the members of them are bound to pray continually for the good or prosperity of all the churches of Christ in all places, and upon all occasions to further it (every one within the bounds of their places and callings, in the exercise of their gifts and graces), so the churches themselves (when planted by the providence of God so as they may have opportunity and advantage for it) ought to hold communion amongst themselves for their peace, increase of love, and mutual edification.

26. In cases of difficulties or differences, either in point of doctrine or in administrations, wherein either the churches in general are concerned, or any one church, in their peace, union, and edification, or any member or members of any church are injured in or by any proceeding in censures not agreeable to truth and order, it is according to the mind of Christ that many churches holding communion together do by their messengers meet in a synod or council to consider and give their advice in or about that matter in difference, to be reported to all the churches concerned. Howbeit, these synods so assembled are not entrusted with any church power properly so called, or with any jurisdiction over the churches themselves, to exercise any censures, either over any churches or persons, or to impose their determinations on the churches or officers.

27. Besides these occasioned synods or councils, there are not instituted by Christ any stated synods in a fixed combination of churches or their officers in lesser or greater assemblies, nor are there any synods appointed by Christ in a way of subordination to one another.

28. Persons that are joined in church fellowship ought not lightly or without just cause to withdraw themselves from the communion of the church whereunto they are so joined. Nevertheless, where any person cannot continue in any church without his sin, either for want of the administration of any ordinances instituted by Christ, or by his being deprived of his due privileges, or compelled to anything in practice not warranted by the Word, or in case of persecution, or upon the account of conveniency of habitation; he, consulting with the church, or the officer or officers thereof, may peaceably depart from the communion of the church wherewith he hath so walked, to join himself with some other church where he may enjoy the ordinances in the purity of the same, for his edification and consolation.

29. Such reforming churches as consist of persons sound in the faith, and of conversation becoming the gospel, ought not to refuse the communion of each other, so far as may consist with their own principles respectively, though they walk not in all things according to the same rules of church order.

30. Churches gathered and walking according to the mind of Christ, judging other churches (though less pure) to be true churches, may receive unto occasional communion with them such members of those churches as are credibly testified to be godly and to live without offense.