After he retired, Schaeffer remained in the Rockies organization as a coach.[4] Schaeffer was named the manager of the Asheville Tourists for the 2015 through 2017 seasons, and the Hartford Yard Goats for the 2018 and 2019 seasons.[5] He was named the manager of the Albuquerque Isotopes for the 2020 season,[6] which was cancelled due to the COVID-19 pandemic. He returned to manage Albuquerque in the 2021[7] and 2022 seasons.[8]
On November 7, 2022, the Rockies promoted Schaeffer to their major league coaching staff as their third base and infield coach for the 2023 season.[9]
Personal life
Schaeffer's wife, Callie (née Rhodes), played softball at Virginia Tech.[4] They have two children.[10]