But none of his onfield battles were ever as difficult or challenging as his fight against cancer.
It was a random drug test taken after the 1999 Scottish Cup final - A game Celtic lost 1-0 to their greatest rivals - that revealed Stubbs's problem.
As he hadn't taken anything the result pointed in an unwelcome direction. Testicular cancer.
Stubbs would have to undergo an operation to remove a testicle and then a savage bout of chemotherapy and a further operation when the disease returned in 2000.
"Whenever anyone says that big C word a black hole opens up in front of you and you feel as if it's just a matter of time before you're going to be in it," Stubbs says today, as he sits in his office at Everton's training ground Finch Farm.
But, he says his sportsman's mentality meant he was always positive during those dark days.
And, he points out, the survival rates for testicular cancer are very high. "The earlier you can do it the better chance you have of surviving."
Stubbs has now written about his football and medical experiences in a new book, How Football Saved My Life.
It's more than a decade since his original diagnosis but it took this long for him to feel he could look back on those days.
"I sometimes think you look for distance. But the distance is always short because obviously it's a very prominent fact that's happened in your life.
"The way I look back now is I look at myself as really lucky."
"I'd been asked to do this book for the last few years but I didn't think it was the right time. I didn't feel I was ready.
Now he's hoping the book might inspire others who have been touched by the disease as he was when he read Lance Armstrong's biography.
"I was just so disappointed when all the revelations came out that he was taking drugs. There are two separate issues because you can't take away what he went through.
But you can't condone what he did to get back to the top again. At the end of the day he was still a sufferer. I respect him because of that. But I don't respect him as a sportsman."
It's as a sportsman Stubbs will be remembered for. He saw Celtic through the best and worst times, and the best and worst managers.
Tommy Burns signed him for Celtic and he joined a team that included Malky McKay and Paolo Di Canio. He was sent off on his debut, and played against Paul Gascoigne in those early Old Firm clashes as Rangers equalled Celtic's nine-in-a-row title run.
He experienced the joy of winning under Wim Jansen and the miseries of the Jozef Venglos and John Barnes eras. And before he moved down south he saw the start of Martin O'Neill's tenure.
Contentiously, he suggests that all too often referees in Scotland are biased towards one side or other of the Old Firm.
And mostly on the blue side. "I stand by that. I always got the impression we were always on the wrong end of quite a few decisions. Probably 50-50 decisions that always seemed to go the other way."
Don't all footballers say that? "I think they do, but I think an Old Firm game is different."
These days Stubbs is coaching the Under 21s and reserves for his home team Everton. (In Liverpool, at least, he's always been a blue).
He is hoping to go into management, but for the moment he's enjoying learning from Roberto Martinez after years spent working with David Moyes.
"Everton have probably lost one of the best managers in the country, that's fair to say."
But right now he's hoping that people will read his biography and draw the same inspiration from it than he got from the Armstrong biography.
"I went through all the emotions writing the book and I hope people enjoy it.
"And the biggest thing for me is I've done the book for the right reasons," he added.
How Football Saved My Life, by Alan Stubbs is published by Simon & Schuster, priced £18.99