The narrator introduces the setting for the story: a village known as Valverde de Lucerna, where a bishop is beginning the beatification process for a saint known as Don Manuel. The narrator introduces herself as Angela Carballino, and says that this nivola will be her confession regarding Don Manuel, whom she regards as her "true spiritual father." Having set the stage for her narrative, Angela begins recounting her memories as a youth in Valverde de Lucerna.
As a child, Angela hardly knew her biological father. Her father was an "outsider" who came from outside of Valverde de Lucena, and he had many books, including Don Quixote as well as histories and classical dramas. Curiously, her mother never said much about her father, considering Don Manuel to be much more important. When she was 10 years old, Angela was sent to Catholic school in the provincial city of Renada. She remembered Don Manuel, who was 36 years old, as tall, slender, and dignified, with a stature like the Buzzard's Peak mountain and eyes like the village lake. At the time, Angela's brother Lazaro lived in America and sent money to Angela's family. At Catholic school, Angela became good friends with several girls from the city, while still keeping in touch with her village friends. Angela stayed at school for five years, and planned to be a teacher, but she soon lost interest in pedagogy.
Returning to Valverde de Lucerna at age 15, she found that Don Manuel had been hard at work in her village, having turned down a prestigious ecclesiastical career to stay and serve the villagers. He spent his time healing marriages, reconciling broken family relations, and helping those about to die. On one occasion, Don Manuel convinced Perote, a man, to adopt his former girlfriend's son as his own. Angela says that today, many years later, a now-paralyzed Perote is being cared for by the very son Don Manuel had convinced him to adopt. In another instance, Don Manuel convinced the villagers that the lake was a sacred place with the power to cure those possessed by the devil. According to Angela, the combined effect of Don Manuel's presence, his words, and his voice were enough to heal the villagers' various ailments—although, she thinks the villagers were likely not possessed, but merely overexcited or epileptic. Don Manuel also desired for the villagers to be well-dressed. As such, he often made sure that those with torn clothing went to the tailor, and he collected clothing from villagers with shirts to give them to those without.
There was another villager in Valverde de Lucerna, a mentally disabled man known as "Blasillo the Fool." Though Blasillo was considered sinful by many other villagers, Don Manuel showed him the most compassion and love out of any in the village, even taking the time to teach Blasillo a few things. When Don Manuel, during his sermon on Maundy Thursday, repeated Jesus’s biblical exclamation, crying "My God, My God!, why hast thou forsaken me?" Blasillo discovered he had an uncanny ability to imitate Don Manuel's heart-wrenching cry, moving the villagers to tears with his imitations.
As time went on, Don Manuel's influence began to make itself clear within Valverde de Lucerna, as even criminals begin confessing their crimes before him. However, when asked by a judge to force a thief to confess, Don Manuel refused, saying, "Human justice does not concern me. This is between him and God...Our Lord has said to us, 'Judge not, that ye not be judged.' " In addition, because of Don Manuel, everyone in the village began to attend Mass on Sundays, even if just to hear him and see him at the altar. When the congregation chanted the Creed with him in unison, Angela heard the sound of bells, which were said to be submerged in the lake, as well as the voices of villagers who have passed away. Angela says that later, once she learned Don Manuel's secret, the voice struck her as being like a caravan traveling through the desert.
Angela says Don Manuel did not condemn those who were unbelievers, Masons, liberals, or heretics—adding that there were none in her village anyway. Instead, he warned against using bad language and being idle. He agreed with the assertion that idleness is the mother of all evils, and believed that "worst of all, is idle thought." Don Manuel constantly busied himself by helping the people around him, whether by threshing during threshing season, making toys for children, teaching lessons or advice to others, or chopping firewood to warm the poor. However, Angela says she realizes now that Don Manuel fled from idleness and inactivity because he was running away from things he did not want to think about.
Don Manuel also accompanied the doctor on his visits, studying the prescriptions and taking a special interest in pregnancies and the raising of children. He was profoundly affected by the death of children, saying, "A baby that is born dead, or one that dies soon after it is born, as well as a suicide...are the most terrible mysteries to me." However, Don Manuel also said once of a father who committed suicide, that "when he reached the final moment and was about to die, he had undoubtedly repented," and thus was worthy of sacred burial ground. In all things, Don Manuel would say that the most important thing is “for people to be happy, and for them to be content with their lives. Contentment with one’s life is the most important thing. No one should want to die, until God wills it.” Once, during a wedding, Don Manuel said that he wished he could “change all the water in the lake to wine…a wine that no matter how much you drank you would be happy and never get drunk.”
A group of poor circus performers once came to visit the village. While the group’s leader, a clown, was performing, his wife succumbed to her illness and died as Don Manuel watched over her. When the clown learned that Don Manuel helped his wife in her final moments, he tried to kiss Don Manuel’s hand and call him a saint. However, Don Manuel acted first and blessed the clown, telling him that the clown is the true saint for acting to give happiness to others, and that the clown’s wife now rests with the Lord.
Angela comments that she realizes now that Don Manuel’s efforts were all, ultimately, his attempts at escaping himself and his loneliness. However, Don Manuel had often gone alone to an ancient Cistercian Abbey, where Father Captain had committed self-flagellation. Once, Angela had asked Don Manuel why he hadn’t joined a cloister (monastery) and become a monk. Don Manuel responded that it was not only because he wanted to help his widowed sister and her two children, but because for him to live alone would be the death of his soul. Calling Valverde de Lucerna his monastery, Don Manuel continued to say that he must live and die for his people; he would not be able to bear the cross of living by himself.
When Angela went to Don Manuel for her confession, she burst into tears and told Don Manuel that she held doubts about the world. Don Manuel told her that all her worries came from literature, and that she should not believe everything she reads. Angela left the confession feeling greatly consoled. However, when she returned the next time, Don Manuel told her that he was not a wise man, but nothing more than a poor village priest. Additionally, he told her that it was the Devil that was influencing Angela and making her have doubts. Taking courage, Angela told Don Manuel the truth: that her doubts were directed towards him and his faith. However, Don Manuel replied that he and the Devil were not acquainted, causing Angela to leave confused as to why Don Manuel would not believe in the Devil. When they met for a third time, Angela asked Don Manuel if he believed in hell; however, he dodged the question, answering only that for Angela there was no heaven, and that she should not concern herself with whether there was a hell. As time went by, Angela began to develop a motherly love for Don Manuel, and spent many years in his presence.
In this first part of San Manuel Bueno, Martyr, Unamuno introduces Angela Carballino, the narrator, and Don Manuel, the protagonist of the story, as well as the village in which they reside. A few tidbits are given about Angela's background: her father was an outsider who came to the village, and he gave Angela many books. Though these details seem superficial at first, they differentiate Angela just enough from the other villagers, making her well-read and inquisitive from a young age. This difference foreshadows her future education, as well as the religious doubts that stem from her knowledge of the world.
Much of the first part is devoted to the acts of Don Manuel. He is described immediately as "tall, slender, and dignified," a perfect model for the less educated villagers of Valverde de Lucerna to look up to, especially Angela. Don Manuel's physicality is described using the imagery and language of the village; he carries his head "like our Buzzard's Peak mountain carries its crest," and his eyes "were the same deep blue as the waters of our lake." In this way, Don Manuel symbolically becomes the embodiment of the village as a whole.
Don Manuel is consistently drawn as a parallel to Jesus Christ of the Bible. Not only does Don Manuel share the same selflessness and concern for the poor as Jesus, he often alludes to the "burden of a cross to bear," whether in regards to the suffering of himself or others. In addition, Don Manuel performs what appears to be a miracle by the lake, in an incident in which he cures several villagers of their demonic possession. However, Angela notes her skepticism at the true nature of the miracle, stating that she thinks the villagers were merely epileptic or overexcited. This small detail foreshadows the reveal that Don Manuel may be less godly than he seems.
Finally, we learn an important fact about Don Manuel, which is that he struggles with a crippling fear of loneliness. This is the first chink in what appears, thus far, to be Don Manuel's spiritual armor, and raises the slightest of questions as to Don Manuel's motivations for being in the village. All this serves as a setup for the next two parts of the story, building up the rising action towards the impending climax.