The move came as it reported like-for-like Christmas sales had tumbled 3.1% in the six weeks to 4 January.
It was the first Christmas since Morrisons introduced its loyalty scheme Match & More, which it said "launched well" online.
The grocer is now looking to close 10 loss making stores to strip back spend. Dalton Philips, who has been at the helm for five years, will leave the business at the close of the financial year and Morrisons said it is already seeking a replacement.
Clive Black, head of research at Shore Capital. said the management changes were not "wholly unexpected" adding Match & More scheme was "confusing".
Andrew Higginson, who Morrisons confirmed today takes over from Sir Ian Gibson as Chairman, said the business needed "new leadership" for the "next chapter of Morrisons development".
Dalton Philips said: "Over the last five years, we have made many improvements to the business and given Morrisons strong foundations for the future.
"I wish every success to the company and all of my colleagues, who have, and continue to work so hard."
Morrisons declined to confirm at this stage whether management changes would have any impact on the marketing team.