On March 20, 2006, Nationals manager Frank Robinson inserted Soriano in the lineup as the left fielder. Soriano, who since 2001 had played exclusively at second base, refused to take the field, and the Nationals organization threatened him with disqualification, which would have meant forfeiture of his salary, and he would not have received credit for service time in fulfillment of the obligations of his contract. With his contract's service terms officially still unfulfilled, he would then have been ineligible for free agency at season's end. Two days later, Soriano relented and played in left field for the Nationals in their exhibition game against the St. Louis Cardinals. Robinson indicated that he considered Soriano's move to left field to be permanent and would not consider moving Soriano back to second base at any point during the season. In his comments following that game, Soriano indicated that he would accept his new position without further argument. As the season got underway, Soriano began to enjoy his new position, and by the All-Star break he led the league in outfield assists. Soriano made his fifth consecutive All-Star team and became only the third man to start All-Star games for both leagues at two different positions.
The Nationals considered trading Soriano before the deadline on July 31, because he was in the last year of his contract, which would grant him free agency at the end of the season. If the Nationals lost Soriano at the end of the season, they would receive a first or second round draft pick from the team that signed him and a "sandwich" pick between the first and second rounds as compensation. Soriano did not want to engage in contract negotiations during the season. However, Soriano expressed his strong desire to stay with the team. Both fans and players began to be more vocal in their support to keep Soriano. Manager Frank Robinson praised Soriano's leadership in the clubhouse, and further suggested that Soriano should be considered for MVP of the National League. There were plenty of suitors, including sending Soriano back to the Yankees, and the Chicago Cubs and Los Angeles Dodgers were also interested. However, Nationals general manager Jim Bowden felt that what he was offered was not worth trading him. The Nationals hoped to sign him to a long term deal before the season ended but on October 12, 2006 he rejected a $70M deal.
Soriano led all major league second basemen in errors every year from 2001 to 2005 (19 (tied), 23, 19, 23, and 21). In 2006, he was second in the major leagues of all left fielders in errors, with 11, but led all left fielders with 22 assists, 9 double plays, and a 2.29 range factor.