The first part of Baxter's monumental work of Puritan casuistry addresses the duties of the individual soul: conversion, the ordering of heart and conscience, government of thoughts, passions, senses, tongue, and body. Published in 1673, it forms the personal foundation on which the rest of the Directory builds. Baxter wrote it to supply every Christian with a practical manual for obeying God in the full range of life.

The second part of the Directory turns from private duties to the household: marriage, the raising of children, the obligations of servants and masters, and the ordering of family worship and daily life. Baxter treats the family as a little church, and each chapter offers searching practical direction for its governance.

The third part addresses duties within the visible church: worship, baptism, the Christian covenant, avoiding heresy, the ministry, and the union of saints across denominational lines. Baxter's irenic spirit is most visible here, as he navigates disputed questions of church order with an eye to conscience and peace.

The fourth part extends Christian duty into the world: the obligations of rulers, lawyers, physicians, soldiers, and ordinary neighbours; cases of conscience in trade, contract, restitution, and forgiveness; and the proper ordering of love toward all men. Together with the preceding three parts, it completes what Baxter called a full directory for the whole of the Christian life.