The 20-year-old joined Los Boquerones from Valencia in the summer of 2011, and has become a regular fixture in Manuel Pellegrini's starting lineup.
Premier League side Chelsea have been linked with a move for the Spanish Under-23 international, who has a £17.8m buyout clause in his contract.
Husillos confirmed that Isco will put pen to paper on a new deal at La Rosaleda, but refused to rule out a future sale.
"He soon will [sign a new deal]", said the Argentine. "He is a flag bearer of this club and wants to continue here. We understand that the signing of the contract is almost secured.
"Any subsequent sale? We are speaking of things that in football we cannot foresee.
"Life takes many turns. No, nothing had been hinted about Isco, [Jeremy] Toulalan, [Martin] Demichelis, nor is any player certain to stay."
Isco has scored four goals in 20 La Liga appearances this season.