Simon Crisford is to leave his long-standing role as racing manager at Godolphin but will remain with Sheikh Mohammed as his global racing adviser.
Crisford, who has been with Godolphin since its inception, told the Racing Post he was looking for a new challenge.
Last year Godolphin was hit by the Mahmood Al Zarooni drugs scandal that led to the trainer being warned off for eight years.
An investigation led by Lord Stevens at Sheikh Mohammed's request recently concluded Al Zarooni had acted alone.
"Having dealt with the events of last year and seen the Lord Stevens inquiry through to its conclusion, I thought this was a good moment to bring my time at Godolphin to a close," Crisford said.
"I had felt for a while I would like a fresh challenge. I think the time is right for a new start for the stable and for me. Sheikh Mohammed has asked me to take on a new role as his global racing adviser.
"I'm delighted to have accepted that position and I'm very much looking forward to what will be an exciting chapter for me.
"This move has been under consideration for some time. It might have happened sooner, but it was my duty to lead the response to last year's problems."