Jordan Beech, 27, has left Town after four years at the club and three seasons in the first team role after replacing Chris Skitt, who left for Ipswich.
Prior to that he worked in Shrewsbury's academy for just over a season.
It will be a big summer of change at Montgomery Waters Meadow as it was this week revealed Cotterill released 13 members of his first-team squad.
The likes of Dave Edwards, Ro-Shaun Williams and Sean Goss led the list of senior players out the exit door.
And the changes stretch to the coaching team with a new lead physio set to be appointed later in the summer.
Town have yet to officially confirm Beech's departure or given an update on the remainder of the fitness team, including fitness coach Andy Johnson and sports therapist Gregg Jones.
Cotterill is eyeing improvements across the board and raising fitness levels were an immediate target upon his appointment last November.
Meanwhile, departing Town legend Dave Edwards spoke of his immense pride at representing his hometown club in an emotional video released by the club.
Edwards, from Pontesbury, referenced his joy at being 'one of the lucky ones' to make it with the club he loves having first watched from the terraces at Gay Meadow with his brother and dad.
The former Wolves midfielder and Wales European Championship semi-finalist