Daubney handed in his notice last week and his replacement is yet to be announced.
He was Loaded's longest-serving editor, having helmed it for seven years, and was responsible for a number of relaunches.
Loaded suffered a devastating freefall in circulation according to Audit Bureau of Circulation figures for the first half of the year.
Its average issue circulation fell 26.3% year on year to 53,591 copies. A number of other titles were also hit by the impact of the recession on male reading habits.
Loaded was first published by IPC Media in 1994, and edited by James Brown. It launched with the strapline: "For men who should know better".
At its peak throughout 1998, the men's magazine consistently sold more than 450,000 copies a month, but has been battling a series of circulation declines ever since. The titles dipped below 100,000 copies for the first time at the start of 2008.
In a statement released by IPC Media, Daubney said: "Being editor of Loaded has been a blast. But for me, the time seems right to move on to new opportunities and let someone else take over the reins."
Last month, Media Week reported that IPC was preparing to sell Loaded to Vitality.
IPC Media said it had no update to provide on the status of the sale talks.