John Adams had not passed his eight years as vice president quietly. He had made enemies in the Senate because his long speeches and lectures to the Senate angered some and his desire for ceremony often upset the rhythms of the body. Additionally, his party affiliations were troubling, for while he declared himself a strong member of the Federalist Party, he sometimes aligned with the anti-federalists as well. During the second election, in 1792, Adams received seventy-seven votes for vice president, slightly more than his first time around. However, by the time 1796 rolled around, and with Washington set to step down from the presidency, the situation in Washington looked grimmer. The Anti-Federalists even started rumors that the Federalists were attempting to found a dynasty by marrying off Adams' daughter to Britain's King George III!

The 1796 presidential race would be the first contested race for the presidency in the country's history. Despite warning's from the departing President Washington that political parties would destroy the country, the rival camps, the Federalists and the Anti-Federalists (Republicans), lined up behind their respective candidates: John Adams and Thomas Jefferson. Additionally, Thomas Pinckney, a former diplomatic representative to Great Britain and a Federalist, and Aaron Burr, head of a political machine in New York City and a Republican, also entered the race. Jay's Treaty of 1794, which provided for the removal of British troops from lands claimed by America, became a key topic of discussion. While seen as largely unsuccessful then, many would later credit the treaty with preventing yet another war with Britain. Most importantly, perhaps, some viewed it as the beginning of a new Anglo-American alliance, and the French heartily disapproved.

As the election neared, much of New England firmly supported Adams for president and Pinckney for vice president. Although the electors were each allowed to vote twice, some New Englanders decided to withhold a vote from Pinckney in case of a close race, despite the protestations of Alexander Hamilton, who feared that Jefferson would become vice president. Both concerns were warranted as it turned out. Had the New England electors solidly voted for Pinckney he would have won the presidency outright, as several southern states switched to support him at the last moment. The final vote was Adams, seventy-one, Jefferson sixty-eight, Pinckney fifty-eight, and Burr 30. For the only time ever in America's history, the president and vice president were from different parties.

John Adams was inaugurated as president of the United States on March 4, 1797, at Federal Hall in Philadelphia (then the nation's capital). He would spend almost all of his presidency in the old city, while a new capital was built on a swamp in an area named Washington, D.C. Adams moved to the new capital, and the new presidential mansion, in the closing months of his term.

Humbled by his slim electoral victory, Adams began his administration by working for harmony. He reached out to Jefferson, his defeated opponent (and now vice president) and worked to mend fences with his fellow Federalists. With no precedent on how to appoint a new Cabinet, Adams kept Washington's former Cabinet–which was largely Federalist, although perhaps more in favor of Alexander Hamilton than was prudent (Adams would not realize this fact until it was too late). To help ease partisan concerns, Adams appointed his Republican friends Benjamin Rush and Elbridge Gerry to posts in the government.

One issue, however, superseded all others in Adams' administration: pending hostilities with France. The Directory, then the ruling party of France, had ordered attacks on U.S. shipping in response to Jay's Treaty. By June 1797, the French had seized over three hundred American ships. They had broken off diplomatic relations with the U.S., sending its envoy home. Many Americans were growing to see war with France as inevitable, and Adams found himself under increasing pressure to act. Washington had continually pushed neutrality in international affairs, stressing in his Farewell Address that the country should remain free of international entanglements and concentrate on forming a solid government at home. Adams, though, found this advice hard to follow. He began preparations to put the country on a defensive footing while his envoys began trying to work out a deal with France. In January 1798 he proposed the creation of a navy department and asked that Congress appropriate enough money to arm the military for war.

It appeared that war with France was all-but inevitable.