Stanton retired from the AFL in 2017 after 255 games in the red sash, first joining the club via the 2003 National Draft.
The 35-year-old departed Carlton this off-season following four years at Ikon Park as an assistant coach, with the Blues not offering Stanton a new deal for next year.
The Bombers have swooped on Stanton's services to succeed Leigh Tudor at Tullamarine, with Essendon's VFL side amassing two wins from 10 games before the 2021 competition was cut short.
Speaking expressed his delight to return to the Bombers and take charge of their reserves side for next season.
“I’m really excited by the opportunity to coach the Bombers’ VFL side,” Stanton said on the announcement.
“I have so much admiration for this club which I called home for the whole of my playing career.
“It’s clear to see the talent unearthed at the club this year, and I’m determined to facilitate an environment which helps our younger and developing players grow in our VFL program to ensure they’re ready to impact at AFL level.”