On September 26, 2017, a federal appeals court overturned Skelos' 2015 conviction and granted him a new trial. The court found that the jurors in the case were wrongly instructed and were not consistent with a 2016 Supreme Court decision. The 2016 ruling narrowed the definition of what it takes to convict public officials of wrongdoing.

On May 4, 2015, Sen. Skelos and his son, Adam Skelos, were arrested and charged with corruption by U.S. Attorney Preet Bharara. The six-count criminal complaint charged the senator and his son with three counts of extortion, two counts of soliciting bribes and one count of conspiracy. The complaint accused Senator Skelos of using his position in the state Senate to benefit AbTech, an environmental technology company, and the real estate developer Glenwood Management. While neither company was named in the complaint, Senator Skelos agreed to help both companies in exchange for payment. According to the complaint, AbTech made payments to Adam Skelos over the course of several years. While Sen. Skelos was using his political influence to help AbTech Industries win a $12 million storm-water treatment contract in his home district, Adam Skelos allegedly told a witness that if his compensation was not increased, they would block the contract. AbTech was awarded the contract in 2013, and Adam Skelos' monthly compensation was reportedly raised from $4,000 to $10,000. In total, Adam Skelos was allegedly paid almost $220,000 to influence his father's actions. The investigation relied heavily on witnesses from the real estate company and from AbTech, as well as wiretaps of Adam Skelos. After Sen. Skelos was charged, he made the following statement: “ I am innocent of the charges leveled against me. I am not saying I am just not guilty, I am saying that I am innocent. I fully expect to be exonerated by a public jury trial. ” —Sen. Dean Skelos Outside of his job with the State Senate, Skelos had served as "of counsel" at the law firm of Ruskin Moscou Faltischek P.C. since 1994. After his arrest, the law firm announced that Skelos was taking a leave of absence from the firm. According to state records, Skelos had earned between $150,000 and $250,000 per year from the law firm, but public court records showed that he never appeared as an attorney for a client in state or federal court. The news of Skelos' arrest came less than three months after former Assembly Speaker Sheldon Silver (D) was arrested on federal corruption charges. On May 28, 2015, Sen. Skelos and his son, Adam, were indicted by a federal grand jury on six counts of bribery, extortion, wire fraud and conspiracy. The indictment was largely the same as the six-count criminal complaint that charged the senator and his son on May 4, but with one additional accusation. According to a report in the New York Times, the indictment also accused the senator of securing over $100,000 in payments and health benefits from an unnamed medical malpractice insurer. The insurer agreed to provide the senator's son with a no-show job, in exchange for being able to lobby the senator on legislative affairs. On June 1, 2015, Sen. Skelos and his son pleaded not guilty to federal corruption charges. A hearing was scheduled for July 30, 2015, to discuss a date for the trial. On July 21, 2015, federal prosecutors released an expanded indictment that added two new charges of soliciting bribes from a Long Island company in return for favorable legislation. The expanded indictment charged Sen. Skelos and his son with eight counts of bribery, extortion, and conspiracy in total. Federal prosecutors alleged that Sen. Skelos used his position in the state Senate to put pressure on an unnamed medical-malpractice insurance company into giving his son a no-show job with benefits worth more than $100,000. According to the indictment, a week after Adam Skelos began his job at the unnamed medical-malpractice insurance company, his supervisor confronted him about why he rarely came into work. Angry about the meeting, court documents showed that "Adam Skelos called back Supervisor-1 and threatened to 'smash in' Supervisor-1's head and told Supervisor-1 that Supervisor-1 would 'never amount to anything' and that 'guys like' Supervisor-1 'couldn’t shine [Adam Skelos’s] shoes.'" On July 30, 2015, U.S. District Judge Kimba Wood scheduled the trial for November 16, 2015. On December 11, 2015, Skelos and his son were convicted of all eight counts of bribery, extortion, and corruption. Dean Skelos was convicted of using his position in the Senate to benefit three companies—a real estate developer, an environmental technology company and a medical malpractice insurer—in exchange for the companies' agreement to give work to his son. Prosecutors said that the three businesses provided Adam Skelos with about $300,000 and other benefits. On May 12, 2016, U.S. District Judge Kimba Wood sentenced former Sen. Skelos to five years in prison.