Chua was the head coach of the Stag Pale Pilseners in the Philippine Basketball League. He achieved the grand slam during the franchise's debut 1995-1996 season, winning the Reinforced Conference, All-Filipino Cup and the Danny Floro Cup. After two seasons, Stag won four of the six tournaments held.
The Stag franchise was renamed the Tanduay Gold Rhum Masters in the 1997-1998 season, where Chua piloted the team to another grand slam. During the 1998-1999 season, the team emerged as champion during the 1st Yakult-PBL Centennial Cup and runner-up during the 2nd Yakult-PBL Centennial Cup. Shortly after, the franchise would leave the PBL and move to the Philippine Basketball Association, marking the return of Tanduay to the PBA.
While coaching Tanduay in the PBL, he was also an assistant coach for Norman Black with the Pop Cola Panthers in the Philippine Basketball Association.
In 2001, Chua joined the Sta. Lucia Realtors as assistant coach under Norman Black. In 2003, Chua was appointed as head coach and led Sta. Lucia to two semifinal appearances during the season. On February 2007, Sta. Lucia announced that Chua was moved to the position of team consultant and assistant coach Boyet Fernandez appointed as the new head coach.
As Sports Executive and Team Director (2015-Present)
Concurrent with Chua's assumption as team manager of Barangay Ginebra San Miguel, he was appointed as alternate PBA governor representing Ginebra San Miguel, Inc. in the PBA board. On July 17, 2015, The Philippine Star reports of Chua's promotion to full-time PBA governor for GSMI and his appointment as sports director for San Miguel Corporation. In June 2015, Chua was elected as president of the Basketball Coaches Association of the Philippines, succeeding Chito Narvasa. He was succeeded by Louie Gonzales in June 2019. In February 2018, Chua was appointed Special Assistant to the Rector for Sports Development of his high school alma mater, Colegio de San Juan de Letran. On January 21, 2019, Chua was awarded the Danny Floro Executive of the Year for 2018 by the PBA Press Corps. On January 17, 2020, Chua won his 11th championship, in 4 years as a sports director and team manager for San Miguel Corporation, after the Barangay Ginebra defeated the Meralco Bolts in 6 games. It was also the third straight season that the teams he was supervising, all won the PBA Finals.