In June 1782, Jones was appointed to command the 74-gun USS America, but his command fell through when Congress decided to give America to the French as replacement for the wrecked Le Magnifique. As a result, he was given assignment in Europe in 1783 to collect prize money due his former hands. At length, this too expired and Jones was left without prospects for active employment, leading him on April 23, 1787, to enter into the service of the Empress Catherine II of Russia, who placed great confidence in Jones, saying: "He will get to Constantinople". He was granted name as a French subject Павел де Жонес (Pavel de Zhones, Paul de Jones).
Jones avowed his intention, however, to preserve the condition of an American citizen and officer. As a rear admiral aboard the 24-gun flagship Vladimir, he took part in the naval campaign in the Dnieper-Bug Liman (an arm of the Black Sea, into which flow the Southern Bug and Dnieper rivers) against the Turks, in concert with the Dnieper Flotilla commanded by Prince Charles of Nassau-Siegen. Jones (and Nassau-Siegen) repulsed the Ottoman forces from the area, but the jealous intrigues of Nassau-Siegen (and perhaps Jones's own ineptitude for Imperial politics) turned the Russian commander Prince Grigory Potemkin against Jones.
Jones was recalled to St. Petersburg for the claimed purpose of transfer to a command in the North Sea. Other factors may have included the theoretical resentment of rival officers, some of whom were several ex-British naval officers also in Russian employment, who regarded Jones as a renegade and refused to speak to him.
In April 1789, Jones was accused of raping a 10-year-old girl named Katerina Stepanova. She testified to the police that she had been summoned to his apartment to sell him butter, when he punched her in the face, gagged her with a white handkerchief, and vaginally penetrated her; a regimental surgeon and a midwife both examined her and found evidence to substantiate these physical and sexual assaults. There had been a delay on one day in reporting the rape, which meant the case would ordinarily not continue, due to Russian statutory codes considering any such delay evidence of consent, but Catherine intervened directly to allow the legal proceedings to continue.
Jones responded to the allegations by claiming that he had paid the girl for sex several times, denying that he had deprived her of her virginity, and suggesting she was older than 10. However, Jones would later change his story and claim the accusation was entirely false, stemming from the supposed desire of Katerina's mother, Sophia Fyodorovna, to gain financially from a prominent man. He involved the Count de Segur, the French representative at the Russian court (and also Jones's last friend in the capital), who investigated the accusation and suggested to Potemkin that it was false, and that Jones was the victim of a plot by Prince Charles for his own purposes. Jones went on to gather evidence, producing Katerina's father, Stephan Holtszwarthen, to testify in court that his daughter was 12 and that his wife had left him for another man, lived in a brothel, and was herself promiscuous.