Historians have difficulty assessing John Adams's presidency. On the one hand, his aloofness and refusal to enter directly into political conflict probably undermined his effectiveness and cost him his reelection in 1800. His stubborn independence left him politically isolated and alone. Even his own cabinet opposed his policies much of the time. He valued no one's opinion half as much as his own—except for that of his wife, Abigail. As an active party politician who nevertheless distrusted factionalism and many Federalist leaders, such as Alexander Hamilton, Adams seems to have been hopelessly out of place in the partisan-style Republic that he had helped bring to life. Much of Adams's isolation reflected a well-conceived value system in which he believed that the executive branch should stand above politics. He viewed the legislature as subject to corruption and thus refused to work with it on a close basis. He prided himself on never giving into public opinion that conflicted with his principles. Adams counted himself among those natural aristocrats who were born for leadership because of their superior reason and virtue. In this sense, he distrusted the people and feared majority rule. Adams believed that the danger to American society in 1800 came not from excessive authority but from conflict and anarchy. Adams's elite republicanism stood in stark contrast to the more egalitarian Jeffersonian democracy that was poised to assume power in the new century.

On the other hand, most historians agree that Adams was correct in not expanding the naval war with France into an all-out conflict. Another protracted war, especially one so soon after the War of Independence with the populace deeply divided along partisan lines, might have been fatal for the nascent American union. Historians concur that Adams nearly won the election of 1800 and that history might have judged him differently had he completed a second term.

Adams has been justifiably censured for having signed the Alien and Sedition Acts, although it is important to note that he neither openly advocated their passage nor personally implemented them. Moreover, when faced with populist defiance, such as in Fries's Rebellion, he ignored Hamilton's call for a strong show of federal force. In the end, he even pardoned the leaders. Seen in this light, Adams's legacy is one of reason, moral leadership, the rule of law, compassion, and a cautious but active foreign policy that aimed both at securing the national interest and achieving an honorable peace.