In his new role, the former defender will mainly work with the under 16s, but also with other age groups.
Jonno made more than 250 appearances for Blues between 1995 and 2003 and helped the club reach the Premier League for the first time at the end of the 2001/02 season.
Academy manager Kristjaan Speakman says he is extremely happy to have someone of Johnson's calibre, experience and enthusiasm on board.
"We're delighted that Michael has agreed to join the programme, and at present it's a great fit with his other commitments," said Speakman.
"In Michael you have someone with a fantastic knowledge of the game at the highest level, outstanding qualifications and a great personality which can only help the young players.
"What's pleasing is his desire to learn and develop and I think he is looking forward to getting back out on the grass and helping us implement our plans.
"Part of our development strategy is to involve coaches within our schoolboy programme with the appropriate qualifications and a Birmingham City connection to complement our existing staff and Michael certainly fits that criteria."