The former defender made 324 appearances for the Cherries over nine seasons, including four of them as first-team captain. He has worked closely with Hughes for the past four years.
Francis told the club's website: "I'd like to thank Bill Foley and Neill Blake for the opportunity to become the first-team technical director of the football club that has been my life for the past 13 years.
"Having been a part of the huge success the club enjoyed during my playing career, I have also been privileged to be a part of the recruitment department, transitioning from Premier League player to a senior scouting role, and then for the last three years as assistant to Richard.
"I can't thank Richard enough for giving me the guidance and tutelage to understand what it takes to operate at the highest level of football. He is someone I will always hold in the highest of regards. From playing together in the same Eddie Howe team to working together off the pitch has been the perfect apprenticeship for me.
"But now I am proud to be able to play a part in the next chapter of this exciting, ambitious football club and look forward to continuing the work with Andoni and this group of players to help the club build towards an exciting future on and off the pitch."
AFC Bournemouth owner and chairman Bill Foley said: "Simon has been a key part of our success, firstly with his performances on the field before working closely with Richard and Neill for the last three years off it.
I'm excited for him to continue that great work, as we aim to sustain our position in the top flight and develop the squad even further over the coming years."
Adding to the comments, the departing Hughes explained: Simon is a true club legend with an unsurpassed knowledge of what it requires to be a success on the pitch for this club and its loyal supporters.
In the four seasons since his retirement from playing he has worked with enthusiasm and purpose behind the scenes to help the team get back to the levels achieved when he was club captain.
With a humility to learn and a selflessness to help others, he is the ideal person to step into the role of first-team technical director and help continue the progressive trajectory the club is on."