Thompson had been out of action – riddled with back pain from a prolapsed disc – as the Bombers face the biggest scandal in their history.
It's understood he returned to work on Friday and was spotted arriving at the club on Monday morning, just as players hit the track for training.
Thompson is the subject of media scrutiny over his role in the hiring of Dean Robinson, the club's high-performance manager who has been stood down while the AFL and Australian Anti-Doping Agency inquiry continues.
Robinson worked alongside controversial sports scientist Stephen Dank, who parted ways with Essendon last year.
Dank declares innocence
Despite speculation about his own future, James Hird was in full control of the training session.
Meanwhile, the parents of all Essendon players have been invited for an information session at Windy Hill on Monday night.
The club will brief the parents on the state of the ASADA investigation into their sons.
Footy's drug crisis as it unfolded
Essendon legend Tim Watson, father of skipper Jobe, will be attending with his wife Susie.
"There are lots of questions that I'm sure lots of parents will have," Watson said on SEN radio on Monday morning.
"There's really one major question for me as a parent. How is it possible the players may have taken substances they didn't consent to?"
Matt Thompson is a reporter for AFL Media. Follow him on Twitter @MattThompsonAFL
