Flores was appointed as Cosmin Contra's successor in January and has guided the club to four wins from 11 subsequent matches in all competitions.
"I wanted to communicate that today's decision to cease my position as coach of Getafe, is a personal decision," he said.
"I think it's the best decision, the best way to dignify my profession, and somehow respect myself.
"I would like to thank everyone from the sporting director to the president, backroom staff, club staff... and above all the players."
Former Atletico Madrid coach Flores leaves the club 13th in La Liga and four points clear of the relegation zone.
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