Hampered by off-field financial trouble, the former Premier League side will feature in the third-tier of English football for the first time since the 1992-93 campaign next year.
Twenty points adrift of safety at the bottom of the table, the club are no longer able to survive the drop following Monday night’s 4-1 defeat to Derby County.
The north west club have won just four of their 41 league games this season in a campaign to forget both on and off the field.
Neil Lennon left his post as manager in mid-March, with the former Celtic coach unable to improve the team’s fortunes after being marred by background distractions.
Following confirmation of their descent into League One, skipper Pratley admitted he expected there to be wholesale changes at the club, with Bolton desperate to bounce back at the first time of asking.
"Every day there is something negative coming out of the club and it needs a whole new change, probably a whole new squad," the 30-year-old midfielder told BBC Sport.
"Upstairs the finances seem like they're sorted now and there needs to be a positive vibe around the whole club as the last couple of years have been negative.
"Everything that has been going on, obviously it has been in the changing room whether you want it to or not - you can come out and say it doesn't affect you but it does."