Huistra began his coaching career in 2001 as Head Coach of Jong Groningen which he was for four years. On 1 July 2005 he left Groningen and was named as the new assistant coach of Aad de Mos at Vitesse. After Vitesse he became an assistant coach at AFC Ajax as replacement of the injured Rob Witschge and was named as the new Jong Ajax Head Coach on 24 April 2009, he signed a contract between 30 June 2011. On January 2010, after FC Groningen coach Ron Jans announced his intention to leave the club at the end of the season, Huistra was announced as new team head coach for the 2010–11 season.
He served as head coach for two full seasons, the final one being particularly disappointing as his Groningen team failed to enter the race for a UEFA Europa League spot and instead narrowly escaped relegation by the end of the season; the seasonal outcome, well below the board aspirations, led to his dismissal on 10 May 2012.
On 30 May 2012 he was announced as new head coach of recently relegated 2012–13 Eerste Divisie club De Graafschap, with the goal to bring his new club promptly back to the top flight. He was fired on 24 December 2013, as of a lack of good results in the past weeks.