Many appeals in state and federal courts followed. Davis and his lawyers argued that the racial composition of the jury and poor advocacy from his lawyers had affected his right to a fair trial. Seven of the original nine eyewitnesses who had linked Davis to the killing recanted all or part of their trial testimony. Several stated they had felt pressure by police to implicate Davis. New witnesses implicated Coles in the crime. The appeals were denied with courts declaring that Davis had not provided a "substantive claim" of innocence and that the recantations were unpersuasive. In July 2007, September 2008, and October 2008, execution dates were scheduled but stayed shortly before the events took place.
In August 17, 2009, the U.S. Supreme Court, over the dissenting votes of two justices, ordered a federal district court in Georgia to consider whether new evidence "that could not have been obtained at the time of trial clearly establishes [Davis'] innocence". The evidentiary hearing was held in June 2010, during which several former prosecution witnesses recanted their previous testimony and described police coercion. Other witnesses asserted that Coles had confessed to the killing; this evidence was excluded as Coles was not given the opportunity to rebut it. In an August 2010 decision, the conviction was upheld, with the U.S. District Court for the Southern District of Georgia declaring that the new evidence cast only "minimal doubt on his conviction". Subsequent appeals, including to the Supreme Court, were rejected, and a fourth execution date was set for September 21, 2011. A clemency hearing by the Georgia Board of Pardons and Paroles was set for September 19. Over 650,000 people signed a petition urging the Board to grant clemency. On September 20, the Board denied him clemency.
In December 2001, Davis filed a habeas corpus writ in the United States District Court. He submitted exculpatory affidavits that contained recantations of testimony of prosecution eyewitnesses, the testimony of a previously undiscovered eyewitness and others with information bearing on the crime. From 1996 onwards, seven of the nine prosecution witnesses recanted all or part of their trial testimony. Dorothy Ferrell, for example, stated in a 2000 affidavit that she felt under pressure from police to identify Davis as the shooter because she was on parole for a shoplifting conviction. In her affidavit, she wrote: "I told the detective that Troy Davis was the shooter, even though the truth was that I didn't know who shot the officer." In a 2002 affidavit, Darrell Collins wrote that the police had scared him into falsely testifying by threatening to charge him as an accessory to the crime, and asserted that "I never saw Troy do anything to the man (Larry Young)." Antoine Williams, Larry Young and Monty Holmes also stated in affidavits that their earlier testimony implicating Davis had been coerced by strong-arm police tactics. In addition, three witnesses signed affidavits stating that Redd Coles had confessed to the murder to them. The State of Georgia argued that the evidence had been procedurally defaulted since it should have been introduced earlier, and this position was accepted by the judge in May 2004, who stated that as the "submitted affidavits are insufficient to raise doubts as to the constitutionality of the result at trial, there is no danger of a miscarriage of justice in declining to consider the claim." He also rejected other defense claims about unfair jury selection, ineffective defense counsel and prosecutorial misconduct.
The decision was appealed to the 11th Circuit Court, which heard oral arguments in the case in September 2005. On September 26, 2006, the court affirmed the denial of federal habeas corpus relief, and determined that Davis had not made "a substantive claim of actual innocence" or shown that his trial was constitutionally unfair; in addition, neither prosecutors nor defense counsel had acted improperly or incompetently. A petition for panel rehearing was denied in December 2006.
Legal experts argued that a major obstacle to granting Davis a new trial was the Antiterrorism and Effective Death Penalty Act of 1996, passed after the Oklahoma City bombing, which restrained federal courts from overturning death penalty convictions, and ordering new trials. Legal authorities have criticized the restricting effect of the 1996 Act on the ability of wrongfully convicted persons to prove their innocence.
On August 17, 2009, the Supreme Court ordered the Savannah federal district court to "receive testimony and make findings of fact as to whether evidence that could not have been obtained at the time of trial clearly establishes [Davis'] innocence." Justice John Paul Stevens, joined by Justices Ruth Bader Ginsburg and Stephen Breyer wrote that "[t]he substantial risk of putting an innocent man to death clearly provides an adequate justification for holding an evidentiary hearing." Justice Antonin Scalia dissented, stating the a new hearing would be "fool's errand" because Davis' claim of innocence was "a sure loser." He was joined by Justice Clarence Thomas.
In response to the Supreme Court order, a two-day hearing was held in June 2010 in a federal district court in Savannah in front of Judge William Moore. Former prosecution witness Antoine Williams stated he did not know who had shot MacPhail, and that because he was illiterate he could not read the police statements he had signed in 1989. Other prosecution witnesses, Jeffrey Sapp and Kevin MacQueen testified that Davis had not confessed to them as they had stated at the initial trial. Darrell Collins also recanted his previous evidence that he had seen Davis shoot Cooper and MacPhail. The witnesses variously described their previous testimony against Davis as being the result of feeling scared, of feeling frightened and pressured by police or to get revenge in a conflict with Davis. Anthony Hargrove testified that Redd Coles had admitted the killing to him. The state's lawyers described Hargrove's testimony as hearsay evidence; Judge William T. Moore permitted the evidence but stated that unless Coles appeared, he might give the evidence "no weight whatsoever." Another witness making a similar statement was heard, but a third was rejected by Judge Moore as the claims were inadmissible hearsay because Coles was not called as a witness and given the opportunity for rebuttal. Moore criticized the decision not to call Coles, saying that he was "one of the most critical witnesses to Davis' defense". One of Davis' lawyers stated that the day before they had been unsuccessful in serving a subpoena to Coles; Moore responded that the attempt had been made too late, given that the hearing had been set for months. State attorneys called current and former police officers and the two lead prosecutors, who testified that the investigation had been careful, and that no witnesses had been coerced or threatened. A state attorney asserted that the testimony of at least five prosecution witnesses remained unchallenged, and the evidence of Davis' guilt was overwhelming. In July 2010, Davis' lawyers filed a motion asking Moore to reconsider his decision to exclude testimony from a witness to a confession by Coles, but in August 2010, Moore stood by his initial decision, stating that in not calling Coles, Davis' lawyers were seeking to have only part of the evidence on the matter.
Moore ruled that executing an innocent person would violate the Eighth Amendment, but that Davis and his legal team had failed to demonstrate his innocence. In his decision, Moore wrote: "while Mr. Davis's new evidence casts some additional, minimal doubt on his conviction, it is largely smoke and mirrors." Of the seven recantations, Moore found that only one was wholly credible and two who were partly credible. He did not consider Coles' alleged confessions because of the failure of Davis' lawyers to subpoena Coles, and suggested that Davis should appeal directly to the Supreme Court. In November 2010, the federal appeals panel dismissed an appeal on the case, without ruling on its merits. They stated that Davis should appeal the case directly U.S. Supreme Court "because he had exhausted his other avenues of relief." Rosemary Barkett, one of the panel judges, later released a statement saying that though she agreed with the decision, she still believed that Davis should be given a new trial.