Khomyakov began his coaching career in Uzbekistan with Mash'al Academy in Mubarek, working with youth players. In the 2011 season, he was appointed head coach of the academy's main team. At the beginning of the 2013 season, following his success with the academy, he was appointed head coach of
Mash'al. In 2014, he obtained the
AFC Pro coaching license. He managed Mash'al until 2019. During the second half of the 2019 season, he signed with
Andijan as head coach, but was dismissed at the start of the 2020 season. After a two-year break, he returned to Mash'al as head coach, leaving the post at his own request at the beginning of the
2022 season. In 2022, he worked as an assistant to Viktor Kumikov at Andijan. At the start of the 2023 season, after Kumikov left the club following an offer from Kazakhstan, Khomyakov was appointed head coach of Andijan. Under his leadership, Andijan defeated Navbahor 3–2 in the 2024 Uzbekistan Cup final on 5 October 2024, winning the club's first trophy in its history. Following five consecutive defeats in the 2025 Uzbekistan Super League season, he left his position at Andijan. Since 2025, he has been the head coach of
Bukhara. == Honours ==