[3][7] In 2013, Molloy returned to the WNBL, as head coach of the newly branded Melbourne Boomers.

[8] In his first season back, after leading the Boomers to the semi-finals, he was named the WNBL Coach of the Year for the second time.

[4] At the same time, he served as head coach of the Canberra Gunners in the South East Australian Basketball League.

[18] In November 2021, Molloy was appointed head coach of the Wellington Saints for the 2022 New Zealand NBL season.

[18] As defending champions and the most successful club in NZNBL history with 12 titles, the Saints went 3–7 over the first ten games to be in danger of missing the top six finals for the first time since 2007.

[20] In December 2022, Molloy was appointed head coach of the Southland Sharks for the 2023 New Zealand NBL season.

In 2009, Molloy was appointed head coach of the Australia U-17 men's team, leading into the inaugural FIBA Under-17 World Championship in 2010.

[27] In 2017, Molloy was appointed as assistant coach to Kennedy Kereama with the New Zealand Tall Ferns, leading into the 2017 FIBA Asia Women's Cup.