Prunty served as the Blazers' head coach during the NBA Summer League in 2008 and 2009. He joined the Cleveland Cavaliers as an assistant coach in 2010. On August 20, 2013, he was hired as an assistant coach by the Brooklyn Nets. Nets Head Coach Jason Kidd was suspended for the first two games of the season after pleading guilty to a misdemeanor DWI charge stemming from an incident in July 2012. Therefore Kidd named, Joe Prunty to serve as acting head coach for the team's season opener against Cleveland Cavaliers and their home opener against Miami Heat. In being the acting head coach, Prunty in the two games went 1-1 with a loss against Cleveland and a win against Miami. In the 2014-2015 season, Prunty helped Jason Kidd and the rest of the Bucks coaching staff reach the Eastern Conference Playoffs.