Ali joined EBLEX in January 2005 and has overseen the focused development of the organisation's strategy, governance and activities.
This has included concentrating EBLEX's operational delivery through three core products: "Better Returns", "Sustainable Supply Chains" and "Promoting Profitable Demand."
He said: "This has been an extremely difficult decision to make but I always knew I would want to pursue other challenges and opportunities.
"The move to the new structure seemed like a suitable time for me to entrust the organisation to others as it moves through its transitional phase."
EBLEX chairman John Cross said: "Richard has played an integral role in implementing the board's strategy for the English beef and sheep sectors. I thank Richard for his contribution and support and wish him well for the future."
Plans are being put in place to manage EBLEX on an interim basis from 1 April 2008, until a permanent appointment is made.
The EBLEX Board has now ratified the appointment of Richard Lowe from the Meat and Livestock Commission as Interim Chief Executive for EBLEX, until a permanent appointment is made.