Williams served as a Marine Corps pilot during World War II and the Korean War. He had been classified 3-A by Selective Service prior to the war, a dependency deferment because he was his mother's sole support. When his classification was changed to 1-A following U.S. entry into the war, Williams appealed to his draft board. The board agreed that his status should not have been changed. He made a public statement that once he had built up his mother's trust fund, he intended to enlist. Even so, criticism in the media, including withdrawal of an endorsement contract by Quaker Oats, resulted in his enlistment in the Navy on May 22, 1942.
After retirement from play, Williams helped new left fielder Carl Yastrzemski in hitting. He then served as manager of the Washington Senators, from 1969–1971, then continued with the team when they became the Texas Rangers after the 1971 season. Williams's best season as a manager was 1969 when he led the expansion Senators to an 86–76 record in their only winning season in Washington. He was chosen "Manager of the Year" after that season.
In his last years, Williams suffered from numerous cardiac problems. He had a pacemaker installed in November 2000 and underwent open-heart surgery in January 2001. After suffering a series of strokes and congestive heart failure, he died of cardiac arrest at the age of 83 in Citrus Hills, Florida, on July 5, 2002.
Though his will stated his desire to be cremated and his ashes scattered in the Florida Keys, John-Henry and Claudia chose to have him frozen.