Sanchez Flores communicated his decision to bring an end to his time as coach of Getafe at a press conference on Thursday.
He explained his decision to leave was for personal reasons, and thanked the club for the opportunity they had given him in recent months.
“I want to communicate to you my decision today to stand down as Getafe coach,” Sanchez Flores said in a statement on the club’s official website.
“It is a personal decision, the product of deep reflection which will allow me to avoid situations which at the time did not make me happy.”
Sanchez Flores took charge of Getafe on January 5 this following the departure of Cosmin Contra to Chinese side Guangzhou.
The 50-year-old was in charge for 12 games, winning four, drawing two and losing seven. He leaves them 13th in La Liga, four points above the relegation zone.