He was named the GM of the Philadelphia Phillies on November 3, 2008, succeeding Pat Gillick and remained in that position until September 10, 2015.

Born and raised in the Rhawnhurst neighborhood of Northeast Philadelphia, Amaro played Little League Baseball for Crispin Gardens.

Amaro is Jewish; his mother Judy Amaro-Perez (née Herman)[3] is of Russian-Jewish heritage and his father was a Catholic Mexican-Cuban.

[1] Amaro joined the Phillies front office immediately after his playing career ended in 1998, hired by then-GM Ed Wade.

In late July, when the Phillies were 3+1⁄2 games behind the Atlanta Braves, he pulled off yet another crafty trade, acquiring Roy Oswalt and "triggering a late-season blitz to baseball's best record."

Prior to the 2011 season, Amaro managed to convince Lee – then a free agent courting interest from the Texas Rangers and New York Yankees – to re-sign with the Phillies, joining a pitching rotation consisting of Halladay, Oswalt, Cole Hamels, and Joe Blanton.

[17][19][20] However, Amaro was criticized for giving a US$125 million 5-year contract extension to an already-ailing Ryan Howard in 2010, which was regarded as highly unnecessary, because Howard was already signed through to the end of the 2011 season – by which time he would be 32 years old, which is "about the age at which teams start to worry about decline in big-bodied first-base/DH types.

"[21][22] Further, the latter part of Amaro's tenure as GM was comparatively unsuccessful, as Philadelphia failed to reach the postseason in 2012 and subsequent seasons.

Howard's performance ended up far worse than skeptics expected, and by 2014 Amaro was "trying hard to deal Howard away, expressing a willingness to eat a lot of the money.”[23] Shortly after Amaro fired manager Charlie Manuel, in 2013, Manuel admitted that he had known that the Phillies roster lacked enough "pieces to win" in 2012 and 2013.

[2] Amaro was hired as first base coach by the Red Sox for the 2016 season, returning to the field for the first time since retiring as a player.

[31] Following the 2018 season, the Mets promoted Amaro from the coaching ranks into a front-office advisory role, under new GM Brodie Van Wagenen.

Amaro is co-founder of the Richie Ashburn Harry Kalas Foundation, which provides baseball camps for underprivileged children in the Delaware Valley.

Amaro attended the same school as television and film producer Adam F. Goldberg, on whose adolescence the show is based.