Kenny Bain, European regional manager for Kana, has taken over the role.
Mr Hughes told The Herald in July that he had approached French owner Sword, who bought the business for £30 million in 2008, with a proposal to seek a new US owner to grow and develop the business.
"Our competitors are Oracle, Microsoft and the giants, and I wanted us to get some scale," he said at the time, adding that he expected growth in research and development at the group's headquarters at Inchinnan, Renfrewshire.
Mr Hughes's departure emerged as Ciboodle's 2011 accounts were lodged at Companies House. They show the group, in its final year before being acquired by Kana in July, reversed a £283,000 loss into a £75,000 pre-tax profit.
It increased turnover from £9.7 million to £12.2m last year and cut the operating loss from £347,398 to £62,378, while staff numbers rose from 158 to 180.
The group paid out a £12.6m dividend to Sword days before the transaction was finalised. Its shareholder funds were up from £10.1m to £10.6m.
Kana has made three other acquisitions in 2012 including Lagan Technologies in Belfast.