In the autumn of 2009, he was selected as head coach of HIFK where he led the club towards promotion to the Finnish first division Ykkönen after season 2010.
[5] Soon after he was appointed as the new head coach of HIFK which had faced relegation back to Finnish second division, Kakkonen, after the ending season, led by Honkavaara's successor in the managerial role, Juha Moilanen.
After the 2014 season, HIFK was promoted to Veikkausliiga, making it to the top tier of Finnish football for the first time in over 40 years.
[7] At the end of November 2016 it was announced, that Honkavaara would be the new manager of Kuopion Palloseura (KuPS), starting from 1 January 2017.
The Belgian club offered to pay a €100,000 fee for his contract, but KuPS was reluctant to let Honkavaara leave.
On 20 December 2024, Swedish Allsvenskan side Djurgården announced that they had appointed Honkavaara as their new manager on a three-year contract, starting in January 2025.
Honkavaara has studied Finnish language and literature at the University of Eastern Finland in Joensuu, and has later worked as a teacher.