He had been widely expected to sign a new two-year contract, having led Al Ahli to second place in the league this season, but instead announced he would be leaving with immediate effect.
"I'm really sad... but for me two years is my limit so I feel this is the moment to say goodbye," Flores told a news conference in Dubai.
Flores also won two domestic knockout competitions, the Etisalat Cup and President's Cup.
"With Quique's calibre he will always have job offers from Europe... we tried our best to retain him," said Al Ahli chairman Abdullah al Naboodah.
"We will take a few days to put together a shortlist but it won't be easy to replace him."
Flores's exit follows that of former Italy goalkeeper Walter Zenga, who ended his two-year stint at rival Dubai club Al Nasr by mutual consent earlier this month.
A few days later Sven-Goran Eriksson quit as Al Nasr's technical adviser after just four months to become the coach of China's Guangzhou R&F.
