On September 14, all the prisoners, except one who was too ill to travel, were removed from New Haven to Hartford, the capital of Connecticut, where the trial opened on September 17, with Judge Smith Thompson presiding. After three days of legal battling, the judge rendered his opinion: the Circuit Court had no jurisdiction over the charges of murder and piracy, since the alleged crimes were committed on a Spanish ship and in Spanish waters; the various property claims, including Ruiz' and Montez' claims to the African "slaves," should be decided in a District Court; and the writ of habeas corpus for the release of the small girls was rejected.

As soon as the Circuit Court adjourned, Judge Judson convened a District Court in the same room. He decreed that the property claims needed more investigation, but that the captives could be released on bail, based on their appraised value as slaves on the Cuban market. The defense lawyers rejected this bail formula, which implied that the Amistad Africans were slaves, and the captives were returned to prison.

The interpreter had not been effective during the trial, and the Amistad Committee intensified the search for another who could speak Mende fluently. J.W. Gibbs, Professor of Theology and Sacred Literature at Yale Divinity School, took a great interest in the Amistad captives. He learned to count from one to ten in Mende and, armed with this new knowledge, proceeded to the New York docks, counting to every African sailor he met. His efforts paid dividends when, in early October, he found James Covey, a seaman on the British warship Buzzard, who could understand him. Covey, a Mende, had been captured and sold as a child, but was recaptured by British squadrons and brought to Freetown where he was released. He learned to speak English fluently and joined the British Navy. Professor Gibbs took Covey to see the Amistad captives in the New Haven jail, and the Africans shouted for joy when they heard Covey speak in Mende. They could now relate their version of the events.

Meanwhile, the Amistad Committee was not happy with treatment of the captives, and began efforts to provide for their physical well-being and their intellectual and religious instruction. Rev. George Day, a former professor at the New York Institution for the Deaf and Dumb, was employed to supervise the instruction of the Mende captives by Yale Divinity School students. The teachers began their instruction with simple pictures and sign language. By this time, several captives had already died in custody from the lingering effects of exposure, hunger, and dehydration suffered aboard the Amistad.