Defeat to Arsenal on Tuesday condemned the Latics to relegation and Martinez's future will be on the agenda when he meets with Whelan after Sunday's final game of the season against Aston Villa.
Everton, who are looking to replace Manchester United-bound David Moyes, have been linked with Martinez but Whelan says the Spaniard has a string of suitors.
"We'll have a meeting after the final match and he's so honest he will tell me then whether he is staying or going," Whelan said.
"He has had numerous offers. There's clubs bigger than Everton looking at Roberto every season because he's a quality manager.
"We have a partnership, we have complete trust in each other, that's how we operate. Of course we would love him to stay but what he decides I will accept."
The FA Cup winners must squeeze a Europa League adventure into an unrelenting Championship schedule and Whelan is hopeful of boosting the club's playing staff.
"The first season (after relegation) is the one to get back up - the parachute payment is the biggest and we should have the same core of players," he added.
"We are going to have to have more players - take into account the Community Shield against Manchester United and we could end up playing 60 games. We will need a bigger squad."