In the winter of 1819–1820 the president and Congress engaged in the more serious, protracted conflict over the effort to prevent the admission of Missouri as a slave state. Nearly the whole session was consumed in this bitter controversy while the two houses remained deadlocked. The lower house insisted that slavery be banned as a condition for the admission of Missouri, but the Senate stubbornly rejected all measures imposing restrictions. Although deeply concerned over this issue, which threatened to divide the nation into two hostile sections, Monroe never raised the question with his cabinet prior to the passage of the final compromise, knowing that an agreement on the issue would be impossible. Monroe genuinely believed, and this was a widely held opinion, that the restrictionists, among whose leaders were many former Federalists, were trying to revive the old two-party system on a sectional basis.
Within the framework of the then current interpretation of the relationship between the executive and legislative branches, it was impossible for Monroe to intervene directly in the controversy. From the outset he let it be known that he would veto any measure restricting slavery in Missouri, since this would be contrary to the provision of the Constitution requiring that new states be admitted on an equal footing with the older states. Slavery was a legal institution and imposing limitations on Missouri would deprive that state of the right to determine a basic institution. In opposing restriction, Monroe was not only concerned with the constitutional issue: he shared the common view of many southerners that confining slavery to a few states would ensure its perpetuation. Slavery, he believed, would be more easily eliminated if it were diffused throughout the nation.
Monroe was himself a slaveholder. Like most southerners of the revolutionary generation, he condemned it as evil and anticipated its eventual destruction. He agreed with Jefferson, with whom he corresponded on the subject, that the only solution was the removal of blacks to Africa. He was a member of the American Colonization Society, which had this objective as its ultimate goal, and in 1821 he assisted the society in acquiring title to Liberia as a refuge for freed slaves. It was in gratitude for his efforts that the directors named the capital Monrovia.
While the Missouri debates were raging in Congress, Monroe was kept informed of developments by Senator James Barbour of Virginia. Through Barbour, Monroe let it be known that he would approve Henry Clay's compromise admitting Missouri as a slave state and Maine as a free state and banning slavery in territory north of 36°30'. When Monroe finally consulted his secretaries after the passage of the compromise, he received only a qualified approval.
When the compromise was pending Monroe enlisted the aid of George Hay, his son-in-law (then in Richmond), to calm the Virginia hotheads who loudly talked of secession if southern interests were sacrificed. As Monroe told Jefferson, the plot to destroy the Union had been prevented only by the "patriotic devotion of several members of the non-slave-owning states, who preferred to sacrifice themselves at home, to a violation of the obvious principles of the Constitution." Monroe—and this was typical of most southerners—failed to grasp the intensity of northern antislavery sentiment.
In spite of the furor over the Missouri question and the problems created by the depression, the presidential election of 1820 aroused scant popular interest. Fewer voters turned out than for local elections in which there was a real contest. As the only candidate (there was no caucus, the nomination being left to state legislatures), Monroe received all the electoral votes but one. The only conflict over the election took place in Congress when northern restrictionists objected to the inclusion of Missouri's electoral vote in the final count, since the state had not as yet been formally admitted. The issue was solved by reporting two sets of electoral votes, one with, and the other without, Missouri's three votes. This was by no means the end of the dispute over Missouri. During the session of 1820–1821 there was a prolonged conflict over provisions in the Missouri constitution making it illegal for free blacks to enter Missouri and forbidding manumission without specific authorization of the state legislature. Clay worked out a compromise providing that no provision of the Missouri constitution should be construed as denying any citizen the privileges and immunities of citizens of the United States. While Clay labored in Congress, Monroe quietly helped round up the votes needed to ensure the passage of what has been termed "the second Missouri Compromise."
In view of the responsibility the Constitution assigned to the executive for the conduct of foreign relations, Monroe understandably gave close attention to this aspect of his office. When Monroe and Adams were in the capital, daily conferences were the rule, for the State Department was but a few minutes—walk from the White House. When the president was at Oak Hill during the summer, messengers regularly brought him dispatches. Monroe read all the diplomatic correspondence, scrutinizing and frequently revising Adams' notes.