In 1999, he took over as the head coach for the WNBA's New York Liberty, making his WNBA debut on June 10, 1999 when he guided the Liberty to an 87-60 victory over the defending Eastern Conference champion Cleveland Rockers. With the Liberty posting impressive attendance figures for the third straight season, Madison Square Garden played host to the first-ever WNBA All-Star game - a sellout (18,649) - on July 14, 1999. Four Liberty players were selected to the Eastern Conference squad: Rebecca Lobo, Teresa Weatherspoon, Kym Hampton, and Vickie Johnson.
With Adubato at the helm, the Liberty posted an overall mark of 18-14 and won its first Eastern Conference title. After defeating Charlotte in the first round of the playoffs, the team faced a rematch with the defending WNBA champion Houston Comets. Despite falling short of the title, the series was pushed to a third game when Weatherspoon made the most famous shot in WNBA history -- a half-court, buzzer-beating shot that won Game Two before a stunned Houston squad and Compaq Center crowd.
Under Adubato, the Liberty went to the finals three out of four seasons and won the Eastern Conference regular-season championship three times.
Adubato took over as coach of the Washington Mystics, but left the Mystics on June 1, 2007, reportedly upset over his team's 0-4 start to the season, a number of recent transactions, and his contract status.
Adubato currently serves as the radio color analyst for the Orlando Magic.