The Spain Under-21 star has admitted that both sides are keen to sign him, but he has yet to make a final decision on his future
The 21-year-old has long been linked with a move away from his current club following his fine performances throughout the 2012-13 campaign and he has now admitted that Madrid and City are leading the race for his signature.
"There are two options on the table. I have received offers from Real Madrid and Manchester City," the youngster was quoted as saying by AS.
"I hope to make a decision soon because I still have a contract with Malaga. I have already said before that Madrid and City are both great clubs. I want the best solution for Malaga and for myself.
"It doesn't matter to me who the owner or president is. I just want to play football and have fun. It doesn't matter to me what kind of formation a team plays. I have my own characteristics, but you always have to adapt to your surroundings."
The 21-year-old then went on to discuss his relationship with new Manchester City manager Manuel Pellegrini, who he previously worked with at Malaga.
"I have not spoken to him yet. I heard about his move to City on the Internet. He's a great coach and I hope he will do well in England. He did an impressive job at Malaga and at other clubs in the past, so I have little doubt that he will succeed at City.
"It's a fact that I already know Pellegrini. I know how he works and he has played a key role in my career so far during our two years together at Malaga. It's a plus that I already know him, but there isn't anything definitive as of yet."
Isco's contract with Malaga runs until 2016, but he has a €35 million buy-out clause.