Before the 1999 season, he moved into the front office as an assistant to GM Ed Wade. The situation wasn't much better then. The Phillies were coming off their 11th losing season in 12 years.
A decade later, obviously, the franchise has come full circle. They're about to appear in the World Series for a second straight year for the first time in franchise history.
Amaro is in a unique position to chart the evolution, to note the mileposts that have marked progress along the way. And, in his view, it all started with a couple of names that aren't exactly popular with Phillies fans of a certain age:
Wade and David Bell.
By the time he was let go after the 2005 season, Wade had become a lightning rod for all the frustrations of a fan base that hadn't been able to experience watching its club in postseason play since 1993.
Amaro - Philadelphia native, son of a Phillies player, batboy for the 1980 world championship team - saw something different.
"I just remember when I was growing up here, the glory days of the late '70s and early '80s when we were, like, awesome," he said. "Everybody wanted to be a Phillies fan because we had Boone, Schmidt, Bowa, Trillo, Carlton, Maddox. Some studs, you know? Those are the guys I grew up with. My favorite was Bake McBride. He wasn't there as long but Shake 'n Bake, he was the man. I could identify with those players. And that was really the goal, to try to get back to where our fans would love our players and could identify with a core group of players.
"When Ed set out on the track of being the GM here [in 1998], that's what his goal was. He really started the ball rolling. That's what his goal was. Because he made a lot of changes in player development, he made a lot of changes in scouting."