After serving as an assistant coach in the Sky Blue FC organization for three years, Holly was named head coach in January 2016. He was asked to step down from that position on 16 August 2017, due to complaints of verbal and emotional abuse from players and because his relationship with then team captain,
Christie Pearce, had become disruptive to the locker room. In August 2020, he was hired as head coach of
Racing Louisville. It was revealed following a wider investigation into the NWSL in 2022 that Holly had been fired "with cause" due to alleged sexual abuse, with the report saying former Racing player
Erin Simon had accused Holly of sexual coercion and sexual harassment. According to Yates' report, Holly "repeated the same pattern of misconduct throughout his coaching career at both Sky Blue FC & Racing Louisville." The report says Holly sent Erin Simon explicit photos and also requested that she come to his house to review game film "and showed her pornography, while masturbating in front of her before she left," the report states. The report also found that Holly had never completed the licensing required to coach in the NWSL. ==Personal life==