The Primera Division champions have already rejected bids of ?25million and ?30million from Manchester United and Martino believes the former Arsenal midfielder will continue to fend off their advances to stay at Barca.
"I would prefer him to stay with us and I dare say he will, but it's his decision," Martino told the club's official website.
"He is one of the best players in the squad. I think he will stay. But there's a part that he has to decide.
"Cesc will decide the situation, but it has not occurred to me that I won't be able to count on him."
Fabregas was on the bench for Friday's 8-0 thrashing of Brazilian side Santos at the Nou Camp but came on in the second half alongside new signing Neymar to score twice and set up Jean Marie Dongou for the final goal.
Lionel Messi, Pedro, Alexis Sanchez and Adriano also scored for the Spanish side, along with an own goal by Santos defender Leo.