Following his playing career, Oquendo coached and managed in the Cardinals' Minor League Baseball system in 1997 and 1998, and became their bench coach at the major league level the following year. In 2000, he became the Cardinals' third base coach, remaining in that role until 2015, while helping lead the club to 11 playoff appearances, including World Series championships in 2006 and 2011 and four National League pennants. He missed the 2016 season after sustaining a knee injury that required surgery and rehabilitation; at the time, he was the longest-tenured coach in MLB. In 2017, he began serving as a special assistant to Cardinals general manager Mike Girsch, instructing at the Cardinals training facility in Jupiter, Florida. For the 2018 season, he temporarily returned to the Cardinals major league team to serve as third base coach, and he did so once again for a few games in 2020. He then became the Cardinals' Minor League Infield Coordinator.