On January 10, 1861, the State of Florida voted to secede from the Union, becoming the third state to do so, following South Carolina and Mississippi. Maxwell's exact stance on secession remains unknown to historians, but his support from pro-secessionist state legislators seems to suggest that he was a secessionist. In November 1861, the Florida Legislature elected him to the Confederate States Senate, a position he would serve in until the end of the American Civil War. Maxwell was regarded as an exceptionally practical Senator. Realizing that Florida's main contributions to the war effort were food and manufactured goods, he opposed increased taxes and conscription, both of which he felt would hurt Florida's production value. He also asked Confederate President Jefferson Davis to warn people against planting anything other than food. Despite his practicality, Maxwell was known for his corruptness. In the Senate, he was a staunch supporter of President Davis' power-grabs, and did not oppose his expanding executive authority. In addition, Maxwell was named chairman of a special committee tasked with investigating the Confederate Department of the Navy, which was run by his close friend Stephen R. Mallory. Following the disastrous Battle of New Orleans, the Confederate Navy was blamed due to the failure of the ironclads. Hoping to forestall this, Mallory persuaded the Congress to investigate the conduct of the department instead. With the investigative committee stacked with Mallory's friends, including Maxwell and Representative Ethelbert Barksdale, the committee found no evidence of neglect or ineptitude. On May 10, 1865, Union Brigadier General Edward McCook entered Tallahassee without incident. Ten days later, the American flag was hoisted over the Florida State Capitol and McCook read the Emancipation Proclamation on its steps, officially marking the surrender of Florida.
Later career
After the war, Maxwell remained a very popular figure in Florida. In late 1865, Governor William Marvin, a former judge appointed provisionally by President Andrew Johnson, appointed Maxwell to the Florida Supreme Court. Maxwell would only serve in this position for a year before his resignation, however. Maxwell formed a law partnership with Mallory in 1866, and resumed his presidency over the Alabama and Florida Railroad. When Reconstruction ended following the Compromise of 1877, the Democrats retook control of Florida. As a result, Maxwell was appointed to the First Judicial Circuit Court of Florida by Governor George Franklin Drew that year. He served in this position until 1885, when he resigned in order to attend the state's Constitutional Convention. Maxwell and the other delegates rewrote the Carpetbag Constitution of 1868 and instead replaced it with a new Constitution which heavily restricted the rights of African-Americans. In 1887, Governor Edward A. Perry appointed Maxwell as the eighth Chief Justice of the Florida Supreme Court. He would serve as Chief Justice until 1889, when George P. Raney was chosen to succeed him. Maxwell would remain on the Florida Supreme Court as an Associate Justice until 1891, when he officially stepped down.
After his resignation, Maxwell returned to his private law practice until his retirement in 1896. Maxwell lived the family of his daughter's husband in Chipley, Florida until his death in 1903.
Burial and legacy
Maxwell is buried in St. John's Cemetery in Pensacola. Maxwell's son, Evelyn C. Maxwell, also served as a justice of the Florida Supreme Court. Maxwell's grandson, Emmett Wilson, later represented Florida in the U.S. House of Representatives. His father-in-law, Walker Anderson, and his son, Evelyn C. Maxwell, both also served on the Florida Supreme Court.