During the following year Jones spent much of his time in Paris. Louis XVI. gave him a gold-hilted sword and the royal order of military merit, and made him chevalier of France. Early in 1781 Jones returned to America to secure a new command. Congress offered him the command of the "America," a frigate then building, but the vessel was shortly afterwards given to France. In November 1783 he was sent to Paris as agent for the prizes captured in European waters under his own command, and although he gave much attention to social affairs and engaged in several private business enterprises, he was very successful in collecting the prize money. Early in 1787 he returned to America and received a gold medal from Congress in recognition of his services.
In 1788 Jones entered the service of the empress Catherine of Russia, avowing his intention, however, "to preserve the condition of an American citizen and officer." As a rear-admiral he took part in the naval campaign in the Liman (an arm of the Black Sea, into which flow the Bug and Dnieper rivers) against the Turks, but the jealous intrigues of Russian officers caused him to be recalled to St Petersburg for the pretended purpose of being transferred to a command in the North Sea. Here he was compelled to remain in idleness, while rival officers plotted against him and even maliciously assailed his private character. In August 1789 he left St Petersburg a bitterly disappointed man. In May 1790 he arrived in Paris, where he remained in retirement during the rest of his life, although he made several efforts to re-enter the Russian service.
Undue exertion and exposure had wasted his strength before he reached the prime of life, and after an illness, in which he was attended by the queen's physician, he died on the 18th of July 1792. His body was interred in the St Louis cemetery for foreign Protestants, the funeral expenses being paid from the private purse of Pierrot François Simmoneau, the king's commissary. In the confusion during the following years the burial place of Paul Jones was forgotten; but in June 1899 General Horace Porter, American ambassador to France, began a systematic search for the body, and after excavations on the site of the old Protestant cemetery, now covered with houses, a leaden coffin was discovered, which contained the body in a remarkable state of preservation. In July 1905 a fleet of American war-ships carried the body to Annapolis, where it now rests in one of the buildings of the naval academy.