Boden has guided Knights to third place and second place finishes in the Championship since taking over from Welshman Clive Griffiths.
He has systematically reduced the average age of the squad while returning the Castle Park club to the upper echelons of the second tier following a major dip in performance prior to his appointment.
Boden will take the title of director of rugby moving forward.
Forwards coach Nathan Smith, backs coach Joe Ford, head of strength and conditioning Adam Simpson and academy director Tyson Lewis have all committed their futures to Knights, the club announced this week.
The length of Boden’s new deal was not disclosed.
“As people are aware, I’ve got close connection and affiliation to the club – it’s a club that I care about,” Boden, who played for Doncaster from 2005 to 2012, told Knights’ official website.
"When I sat down with Steve Lloyd and Tony De Mulder two years ago, we put a two-to-three-year plan together and we’re two years in, and we feel like we’ve made a good stride forward in rebuilding the club from where it was.
“Off the back of that, we’re hoping to continue to make strides forward as a club, and I’m really happy and humbled that they would like me to be part of that journey.
“The environment and the culture that the club is trying to create makes it easy for me to turn up to work every day and enjoy it – and that’s testament to the club, the board, the supporters, and all the players and staff.”
Knights finished second in this season’s Championship, just three points behind big-spending Ealing Trailfinders.
The club had applied for promotion to the Premiership in the event of them winning the title but it was rejected by the RFU on the grounds of Castle Park’s capacity being too small.
Boden, who has spoken about his ambition to coach at the top level, returned to Doncaster in 2019 initially as forwards coach.
He was previously forwards coach at Jersey and then head coach at Yorkshire Carnegie.