Spooner joined Premier Foods in 2007 as group supply chain director before becoming ceo at Hovis in April, following the completion of a joint venture deal with investment firm The Gores Group.
He said the decision was for entirely personal reasons and had been particularly difficult to make.
He will remain with the firm until the end of January while it searches for a suitable replacement.
Nish Kankiwala, executive chairman, thanked Spooner for his “outstanding contribution” to Hovis.
“He leaves the business in great shape with Hovis achieving a significant year-on-year increase in profits as the only UK bread brand that is growing,” he said.
“We now have the structure, investment and leadership team in place to build on this momentum and ensure the business goes from strength to strength.”