The former Burnden Park favourite had been in charge of the Under-23s since 2016 but now faces an uncertain future as decisions are taken on the restructure of the academy, which will be downgraded to a category three which does not require football at that level.
Lee is currently on furlough and waiting to hear from Football Ventures on whether he will continue with Bolton, where he has worked since becoming assistant academy director in 2008.
Speaking to the Walking Down the Manny Road podcast, the 52-year-old said he would be open to a new role at Lostock.
"I'm furloughed at the football club, waiting for the opportunity to speak to the powers that be to see where my future lies,” he said.
"Obviously I want to stay at the football club and I'm disappointed that the under-23's have been disbanded because I think it's a great route into first-team football.
"The football club have their reasons for it and I respect those, but I'd love to continue in some capacity.
"I love being out there coaching the players and I believe I can bring a lot to the football club and its future, with the younger players coming through the system."
Lee has sympathy with the situation inherited by Keith Hill this season, which barring a big call from the EFL looks certain to end in relegation to League Two.
He maintains ambition to manage a club himself, however, once football returns to some sort of normality.
"He (Hill) has had a difficult start because of the 12-point deduction," he said. "It was always going to be difficult for him.
"He's brought his own players in and tried to get a winning formula.
"He's had good times, indifferent performances, and that's not his fault. Sometimes that's the players just not performing.
"From a perspective of 'would I like to be manager of a football club?' - of course I would. I'm in football because I love it.
"That's not me saying I want to go and pinch Keith Hill's job - I just want to be a manager. I think I've got the credentials and the experience now.
"Whether that be here or at another football club, I want to be a manager."