The former England defender had been one of Tony Pulis’ assistants until the Welshman left the job at the end of the season.
Woodgate’s former Leeds and Tottenham team-mate Robbie Keane will join as his number two along with ex-Boro goalkeeper Danny Coyne and Leo Percovich.
A club statement read: “There was huge interest in the coaching positions following the departure of Tony Pulis and in a robust process the club spoke with a number of potential candidates both in the UK and abroad.
“It was during this procedure that it became clear that Jonathan was the outstanding candidate to head up the new structure, and his staff bring a wealth of experience and knowledge.
“Jonathan’s vision is very much aligned to our own for the club as we look to develop a new identity.”
Woodgate made 112 appearances for Middlesbrough before calling time on his playing career in 2016 to take a job in the club’s academy.
Boro finished seventh in last season’s Championship, one point outside the play-off places.