The book is an account of the memories and legacy of John Ames as he remembers his experiences of his father and grandfather to share with his son. All three men share a vocational lifestyle and profession as Congregationalist ministers in Gilead, Iowa. John Ames describes his vocation as "giving you a good basic sense of what is being asked of you and also what you might as well ignore", explaining that your vocation is something both hard to fulfill and hard to obtain. He writes that this is one of the most important pieces of wisdom he can bestow to his son. Ames's father was a Christian pacifist, but his grandfather was a radical abolitionist who carried out guerrilla actions with John Brown before the American Civil War, served as a chaplain with the Union forces in that war, and incited his congregation to join up and serve in it; as Ames remarks, "He preached this town into the war." The grandfather returned from the war maimed with the loss of his right eye. Thereafter he was given the distinction that his right side was holy or sacred in some way, that it was his link to commune with God, and he was notorious for a piercing stare with the one eye he had left.
The grandfather's other eccentricities are recalled in his youth: the practice of giving all and any of the family's possessions to others and preaching with a gun in a bloodied shirt. The true character and intimate details of the father are revealed in context with anecdotes regarding the grandfather, and mainly in the search for the grave of the grandfather. One event that is prevalent in the narrator's orations is the memory of receiving 'communion' from his father at the remains of a Baptist church, burned by lightning (Ames recalls this as an invented memory adapted from his father breaking and sharing an ashy biscuit for lunch). In the course of the novel, it quickly emerges that Ames's first wife, Louisa, died while giving birth to their daughter, Rebecca (a.k.a. Angeline) who also died soon after. Ames reflects on the death of his family as the source of great sorrow for many years, in contrast and with special reference to the growing family of the Rev. Boughton, local Presbyterian minister and Ames's dear and lifelong friend.
Many years later Ames meets his second wife, Lila, a less-educated woman who appears in church one Pentecost Sunday. Eventually Ames baptizes Lila and their relationship develops, culminating in her proposal to him. As Ames writes his memoirs, Boughton's son, John Ames Boughton (Jack), reappears in the town after leaving it in disgrace twenty years earlier, following his seduction and abandonment of a girl from a poverty-stricken family near his university. The daughter of this relationship died poor and uncared-for at the age of three, despite the Boughton family's well-intended but unwelcome efforts to look after the child. Young Boughton, the apple of his parents' eye but deeply disliked by Ames, seeks Ames out; much of the tension in the novel results from Ames's mistrust of Jack Boughton and particularly of his relationship with Lila and their son. In the dénouement, however, it turns out that Jack Boughton is himself suffering from his forced separation from his own common-law wife, an African American from Tennessee, and their son; the family are not allowed to live together because of segregationist laws, and her family utterly rejects Jack Boughton. It is implied that Jack's understanding with Lila lies in their common sense of tragedy as she prepares for the death of Ames, who has given her a security and stability she has never known before.
Although there is action in the story, its mainspring lies in Ames's theological struggles on a whole series of fronts: with his grandfather's engagement in the Civil War, with his own loneliness through much of his life, with his brother's clear and his father's apparent loss of belief, with his father's desertion of the town, with the hardships of people's lives, and above all with his feelings of hostility and jealousy towards young Boughton, whom he knows at some level he has to forgive. Ames's struggles are illustrated by numerous quotations from the Bible, from theologians (especially Calvin's Institutes of the Christian Religion) and from philosophers, especially the atheist Feuerbach, whom Ames greatly respects.
The abstract and theological content of the book is seen through the eyes of Ames, who is presented in a deeply sympathetic manner and who writes his memoir from a position of serenity, despite his suffering and a knowledge of his own limitations and failings. Throughout the novel, Ames details a reverential awe for the transcendental pathos in the small personal moments of happiness and peace with his wife and son and the town of Gilead, despite the loneliness and sorrow he feels for leaving the world with things undone and unsolved. He is able to revel in the beauty of the world around him and takes the time to appreciate and engage with these small wonders at the end of his life. In this way the novel teaches the importance of stepping back and enjoying present realities. Ames marvels in the every day and commonplace and wishes this attitude for his son, also. He proclaims his desire for his son "to live long and ... love this poor perishable world". Ames takes the time to be fully present and intentional in everything that he does, no matter how small or insignificant it may seem. An example of this from the novel is towards the beginning on page 5 when he passes two young men joking around and laughing with one other on the street and Ames is filled with a sense of awe at the beauty of such a simple expression of friendship and joy. In this way Ames sees the allure in both the ordinary and mundane as well as the tragic. He begins to express a viewpoint that the purpose of life is to look for things to appreciate and be thankful for. In the closing pages of the book, Ames learns of Jack Boughton's true situation and is able to offer him the genuine affection and forgiveness he has never before been able to feel for him.