In 1777, Deane's reputation came under suspicion when his colleague Arthur Lee accused him of misusing government money. Despite these accusations, Deane served alongside Franklin and Lee as an American representative at a 1778 ceremony with French King Louis XVI, celebrating the successfully forged French-American alliance. Several months later, Deane returned to the United States, where he had to answer to the accusations about his finances. Though he tried to defend himself, he faced considerable hostility from Lee and his supporters, including famous patriot Thomas Paine, who denounced Deane as unpatriotic.
Meanwhile, Deane was struggling financially because he had been counting on Congress to reimburse him for work expenses while in France. Although Congress ordered an auditor to assess what was owed Deane, the audit progressed extremely slowly. Deane traveled back to France, and then to Belgium and London, where he received a visit from an old friend, Benedict Arnold. By this point, Arnold had already been exposed as a traitor. Deane's meeting with him further alienated him from Americans, even his former supporters. As his financial position and reputation declined, so did his health. In 1789, he set sail back to the United States but died only four hours after leaving the shore.
In 1841, the audit was finally complete, and Congress granted $37,000 to Deane's descendants.