[2] Ong also coached the club side of Malaysia U-23 squad, Harimau Muda A, who competed in Australia's National Premier Leagues Queensland in 2014.
Despite a series of disappointing results in the 2018 FIFA World Cup qualification, Ong was handed a new two-year contract on 18 January 2016 in charge of the national team.
[6] Ong was re-designated as Malaysia U-22 head coach, replacing Frank Bernhardt, in March 2017 following the appointment of new FAM president Tunku Ismail Idris.
The Football Association of Malaysia (FAM) announced the resignation of Datuk Ong Kim Swee after its technical director accepted the position as the new head coach of Sabah FA.
He guide the team in the league to a third place finished in the 2022 and 2023 season where he also was instrumental in Sabah 2023–24 AFC Cup run until the ASEAN Zonal semi-finals.