Adams's presidency was consumed with problems that arose from the French Revolution, which had also been true for his predecessor. Initially popular with virtually all Americans, the French Revolution began to arouse concerns among the most conservative in the United States after the excesses that commenced in 1792. The King and Queen (Louis XVI and Marie Antoinette) were executed, attempts at de-Christianization occurred, numerous foes of the Revolution—especially aristocrats and monarchists—were executed in the September Massacre (1792) and the Reign of Terror (1793-1794), and the revolutionary leadership moved toward social leveling that would end historic class privileges and distinctions between the social classes. Adams had observed the coming of the French Revolution while living in France and Great Britain, and he immediately realized its potential for terror and anarchy. His skepticism was confirmed.

Nevertheless, the problems that beset Presidents Washington and Adams arose more from the wars spawned by the French Revolution. War erupted in 1792 when France attempted to export its revolutionary ideas and when several European monarchical nations allied against the French, hoping to eradicate the threat posed by the republican revolutionaries. The great danger for the United States began in the spring of 1793 when Great Britain, the principal source of American trade, joined the coalition against France. Although the Washington administration proclaimed American neutrality, a crisis developed when London sought to prevent U.S. trade with France. Numerous depredations occurred on the high seas, as ships of the Royal Navy seized American ships and cargoes and sought to impress American sailors who had allegedly deserted the British navy. Cries for war with Britain were widespread by 1794. Believing that war would be disastrous, President Washington sent John Jay to London to seek a diplomatic solution. The result was Jay's Treaty, signed in 1794. The treaty improved U.S.-British relations. France, interpreting the treaty as a newly formed alliance between the United States and an old enemy, retaliated by ordering the seizure of American ships carrying British goods. This plunged Adams into a foreign crisis that lasted for the duration of his administration. At first, Adams tried diplomacy by sending three commissioners to Paris to negotiate a settlement. However, Prime Minister Charles Maurice de Talleyrand of France insulted the American diplomats by first refusing to officially receive them. He then demanded a $250,000 personal bribe and a $10 million loan for his financially strapped country before he would begin peace negotiations. This episode, known as the XYZ affair, sparked a white-hot reaction within the United States.

Adams responded by asking Congress to appropriate funds for defensive measures. These included the augmentation of the Navy, improvement of coastal defensives, the creation of a provisional army, and authority for the President to summon up to 80,000 militiamen to active duty. Congress passed the Alien and Sedition Acts to curb dissent, created the Navy Department, organized the Marine Corps, and cancelled the treaties of alliance and commerce with France that had been negotiated during the War of Independence. Incidents, some bloody, soon took place on the high seas. Historians call this undeclared war the Quasi-War crisis. Some Americans who hated the French Revolution, especially the Anglophiles within the United States, hoped for war to save Great Britain and destroy the revolutionaries in France. From the outset, however, President Adams sought a peaceful solution, if it could be had on honorable terms for the United States. He talked pugnaciously and urged a military buildup, but his goal was to demonstrate American resolve and, he hoped, bring France to the bargaining table. During the fall of 1798 and the winter of 1799, he received intelligence indicating a French willingness to talk. When Talleyrand sent unofficial word that American diplomats would be received by the French government, Adams announced his intention to send another diplomatic commission to France. By the time the commissioners reached Paris late in 1799, Napoleon Bonaparte had become the head of the French government. After several weeks of negotiation, the American envoys and Napoleon signed the Treaty of Mortefontaine, which released the United States from its Revolutionary War alliance with France and brought an end to the Quasi-War. Adams subsequently said that the honorable peace he had arranged was the great jewel in his crown after nearly twenty-five years of public service.