The Duke of Burgundy was ecstatic that he had finally captured the woman who had caused him and his English allies so much trouble. He put Joan and her squire Jean de Aulon in a cell in his castle at Vermandois. After Joan made an escape attempt, Burgundy thought it best to move her to a more northern castle, farther from French lines. At this castle, Joan made an even more daring escape attempt, leaping sixty feet from the top of her prison tower into the moat. Although knocked unconscious and much bruised from this escape attempt, Joan was not seriously hurt. Burgundy then transferred Joan to a more secure location in Arras.

On May 25, 1430, news reached Paris that Joan had been captured. The University of Paris, which was then pro-English, suggested that Joan be turned over to clergymen for inquisition. Pierre Cauchon, the Bishop of Beauvais, would lead the interrogation, since Joan had been captured in his diocese. On January 3, 1431, Joan was transferred into Cauchon's control for a price of 10,000 francs. She was brought to trial at Rouen, which was then controlled by England's Earl of Warwick.

On January 13, 1431, Joan's trial began; she was tried by the Church (not the State.) Bishop Cauchon and the vice inquisitor of France served as the judges. First, they took statements from various people regarding Joan's reputation as a witch. Joan seemed to meet the standard description: she behaved strangely, she heard mysterious "voices" in her head, she liked to go off by herself for long periods of time, she had unusually good luck, and she usually wore men's clothing. (Indeed, not only had she assumed men's clothing; she had assumed a man's duties and "manly" characteristics, bravely commanding armies and advising male authority figures and even the King himself. Thus in being called a "witch," Joan joined a series of women throughout history who suffered this label for their attempts to transcend traditional gender roles.) On February 21, 1431, Joan herself was summoned before the court. While she did swear to tell the truth, Joan often refused to say anything when she was asked questions which might reveal anything about Charles VII. The original 70 heresy charges shrunk to only 12, and Joan, who had been imprisoned in dank cells for months, now became ill. This worried Burgundy, who wanted to make sure she didn't die before the court could prove she was a witch. Although she feared she was dying, Joan refused to change her statements. Soon, she was allowed to receive communion and to make confessions. On May 23, 1431, the court prepared to transfer her back to secular authorities.

Joan was initially treated well by her captors. John of Luxembourg showed her considerable kindness during his period as her warden. And, although her later jailers were less friendly, they never threatened her life. Why didn't they execute this dangerous woman immediately? They knew that if they simply executed Joan, they would create a martyr for France, and thus create an even more powerful political symbol for the French people to rally behind as they fought against the English. By putting her on trial for witchcraft and heresy, the English-Burgundian forces had a much craftier plan. Most of the leaders didn't really care if she really was a witch or not. Instead, they wanted to undermine her importance with the French people before executing her. Then they would be free to kill her (presumably for religious crimes) without supplying the French with a martyr. They figured that no one would want to side with a convicted witch, so they were happy to turn Joan over to pro-English ecclesiastical forces. Furthermore, by painting Joan as a witch, they would also cast doubt on Charles VII's wisdom as a ruler, suggesting that he had been controlled by a witch in recent years. The way the English-Burgundian allies used the Church to discredit Joan of Arc before killing her shows just how direct and powerful a role religion played in European politics during the 15th century.

During her trial, Joan suffered quite harsh treatment. She wasn't even allowed to attend mass before her trial, one of the few things the ultra-pious Joan begged for. Since Joan had made escape attempts in the past, Bishop Cauchon had her chained to a wooden block, and posted guards who always kept an eye on her.

The fact that Joan constantly refused to talk about matters relating to Charles greatly upset her judges, who formulated 70 charges of heresy against her in a single month. They said her claim to hear divine voices constituted blasphemy. They accused her of claiming to follow the direct command of God from these voices in order to go against the Church itself. They said she indecently wore men's clothes, and falsely claimed to be assured of salvation. They even accused her of a sinful suicide attempt, arguing that she could not have leapt from the sixty-foot tower and truly expected to live. Throughout her questioning on these charges, Joan gave such skillfully evasive answers. When she refused to change her answers at their promptings, her captors became increasingly frustrated, and they threatened her with torture. But Joan stood so adamantly by her story that the court decided that torture would be useless, and in the end the majority of the charges were dropped. Only twelve remained.