After the retirement, Miyamoto started coaching career at Gamba Osaka in 2015. He became a manager for Gamba Osaka U-23 in 2017. In July 2018, top team manager Levir Culpi was sacked when the club was at the 16th place of 18 clubs. Miyamoto was named new manager as Culpi successor. Miyamoto raised Gamba to the 9th place in 2018 season. In 2020, the club won the 2nd place in J1 League and Emperor's Cup.