Iniesta's current deal at the Camp Nou expires in 2018 and the experienced midfielder is yet to put pen-to-paper on an extension, leaving doubts over his future at the club.
The Spain international, who played a key role in helping his country win the 2010 World Cup, has also previously said he could leave if he believes the timing is right.
He still remains an integral part of the first team for the Catalans and the 32-year-old's appearance in Sunday's 4-2 win over Valencia was his 15th league outing of the season.
Many fans are worried about Iniesta's situation but Fernandez, who was appointed sporting director in 2015, is adamant the club legend will extend his stay beyond 2018.
He told Movistar: "We want Iniesta to continue with us for many years to come. I hope he will be with us for a long time. I have no doubt that he will. I have no doubt that it will be so."