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After the expiration of his term, a disappointed Van Buren returned to his estate of Lindenwald in Kinderhook, New York, where he continued to closely watch political developments, hoping to return to the White House in four years' time. He watched with interets the battle between Henry Clay and President John Tyler, who took office after the death of President William Henry Harrison in April of 1841. During this period of political exile, Van Buren made a number of moves calculated to maintain his support in the Democratic Party. He made a trip to the South and traveled to Nashville where he met with Jackson, as well as with former Speaker of the House James K. Polk. The three began thinking about a return to the White House for Van Buren, with Polk as a possible running mate. There were a number of other possible candidates, including Tyler, James Buchanan, Levi Woodbury, Lewis Cass and others. One of these was Jackson's first Vice-President, powerful South Carolina Senator John C. Calhoun.
Van Buren kept his head down and remained silent on a number of major public issues, like that of tariffs. When President John Tyler made annexation of Texas his chief foreign policy objective, thinking that it might be the issue that got him re-elected, many Democrats, particularly in the South, were anxious for the annexation to succeed. When an explosion on the USS Princeton killed Secretary of State Abel P. Upshur in February 1844, Tyler selected Calhoun as Upshur's replacement. Like Tyler, Calhoun was also anxious for the annexation of Texas. Calhoun negotiated an annexation treaty between the United States and Texas.
Van Buren had hoped that he would not have to take a public stand on the issue, but there was no escaping the Texas question. It soon became the central issue in U.S. politics. Van Buren had to make his views on the issue public. Van Buren knew that his public acceptance of annexation would likely help him win the 1844 Democratic nomination, but he also thought that annexation would inevitably lead to an unjust war with Mexico. It seems that principle prevailed over politics and in a public letter published shortly after Henry Clay also announced his opposition to the annexation treaty, Van Buren made his views on the Texas question public, essentially agreeing with Clay's assessment.
Van Buren's opposition to immediate annexation cost him the support of many pro-slavery Democrats. He was still the leading contender for the nomination, but he needed two-thirds of the votes of delegates to win it. In the weeks before the 1844 Democratic National Convention, Van Buren's supporters were able to do the math, and they too realized that their candidate would win a majority of the delegates on the first presidential ballot, but would not be able to win the support of the required two-thirds of delegates. His supporters tried unsuccessfully to change the rules to one of a simple majority, but several Northern delegates joined with Southern delegates in implementing the two-thirds rule for the 1844 convention. Van Buren won 146 of the 266 votes on the first presidential ballot, with only 12 of his votes coming from Southern states. When the convention reconvened and held another ballot, James K. Polk, who shared many of Van Buren's views but favored immediate annexation, won 44 votes. On the ninth and final ballot of the convention, Van Buren's supporters withdrew the former president's name from consideration, and Polk won the Democratic presidential nomination.
One again disappointed by the outcome, Van Buren endorsed Polk in the interest of party unity. He also convinced Silas Wright to run for Governor of New York so that the popular Wright could help boost Polk in the state. Wright narrowly defeated Whig nominee Millard Fillmore in the 1844 gubernatorial election, and Wright's victory in the state helped Polk win it in the electoral college, permitting him to narrowly defeat Henry Clay in the 1844 presidential election.
After taking office, Polk offered Van Buren the ambassadorship to London. Van Buren declined. Although Polk also consulted Van Buren in the formation of his cabinet, the President offended Van Buren by failing to appoint a New Yorker to post of Secretary of State or Secretary of the Treasury. Other patronage decisions in New York also angered Van Buren and Wright.
At the time, the two main factions in the New York Democratic Party were the Barnburners (the anti-slavery faction) and the Hunkers (the faction more tolerant of slavery). Van Buren had tried to keep the peace between the two factions, but after Polk's election, Van Buren became aligned more closely with the Barnburners. The split in the state party worsened during the Polk's presidency, as his administration lavished patronage on the Hunkers.
In his retirement, Van Buren also grew more personally opposed to slavery. His change of heart was partially the result of the Mexican–American War, which he had predicted and tried to prevent. US victory in the war brought the debate over slavery in the territories to the forefront of American politics once again. Van Buren published an anti-slavery manifesto in which he rejected the notion that Congress did not have the power to regulate slavery in the territories, and argued the Founding Fathers had favored the eventual abolition of slavery. This document became known as the "Barnburner Manifesto". He was helped in its composition by John Van Buren and Samuel Tilden, both of whom were leaders of the Barnburner faction.
Following the publication of the Barnburner Manifesto, many Barnburners urged the former president to once again run for President in the 1848 presidential election. The 1848 Democratic National Convention seated competing Barnburner and Hunker delegations from New York, but the Barnburners walked out of the convention when Lewis Cass was nominated as the party's presidential candidate on the fourth ballot. Cass had called for congressional regulation of slavery in the territories.
The Barnburners began to organize as a third party. At a convention held in June 1848, in Utica, New York, they nominated Van Buren for president. He expressed some reluctantance to leave the Democratic Party, but after considering the matter, Van Buren accepted the nomination. He saw his duty as being the need to add his considerable influence behind the power of the anti-slavery movement, hoping to help defeat Cass, and weaken the Hunker faction in New York. At a convention held in Buffalo, New York in August 1848, a group of anti-slavery Democrats, Whigs, and members of the abolitionist Liberty Party met in the first national convention of what became known as the Free Soil Party.
The convention unanimously nominated Van Buren, and chose Charles Francis Adams as Van Buren's running mate. In his public message accepting the nomination, Van Buren expressed his full support for the Wilmot Proviso (proposed legislation that would ban slavery in all territories acquired from Mexico in the Mexican–American War, named for its sponsor, Congressman David Wilmot of Pennsylvania).
Some Free Soil leaders were optimistic that Van Buren could win a handful of Northern states. Their hope was that there would be no candidate with a majority of electoral votes, and this would then force a contingent election in the House of Representatives. The plan failed. Van Buren did not win a single electoral vote. Zachary Taylor was elected President, receiving 163 electoral votes to 127 for Cass. However Van Buren has some success. His nomination helped bring about Cass's defeat by causing the defection of many Democrats from Cass to Van Buren in the North. Van Buren also won over ten percent of the national popular vote and fifteen percent of the popular vote in the Northern states. He was the first third party candidate in U.S. history to win at least ten percent of the national popular vote. In concurrent congressional elections, former Ohio Democrat Salmon Chase won election to the Senate and about a dozen Free Soil candidates won election to the House of Representatives.
Van Buren never sought the presidency again. But he did keep interested in national politics and managed to outlive all four of his immediate successors: Harrison, Tyler, Polk, and Taylor. He died of bronchial asthma and heart failure at his Lindenwald estate at 2:00 a.m. on July 24, 1862, at 79.