The Owls, who were relegated to the third tier of English football at the end of last season, have suffered financially due to the pandemic.
They are still paying a number of their players late wages, but will see several high earners depart at the end of the month which is tipped to help the issue.
Prutton, who represented the club between 2011 and 2014, feels that though Sheffield Wednesday will be a big name for players in League One, uncertainty over wages could ultimately prove to be a deterrent.
“If you are a footballer, you have to look at it purely from a business point of view”, Prutton told The Star.
“Yes it might be glorious playing for Sheffield Wednesday, and it is, but nobody does it for free.
“A fan’s take on that, there’s always the assertion that they would play for nothing and I understand that.
“But when it’s your job or it’s your career, that’ll be something that’ll be heavily thought out by anyone they approach.
“It’ll definitely come into it and hopefully, they’re able to sort it out and draw a line under it.
“If you’re coming at it purely from the angle of playing for a club like Sheffield Wednesday, especially at that level, it will be a huge draw in that division and the sort of players they will be hoping to attract.
“But they have to get their house in order.”
Ten players are set to leave Hillsborough when their contracts expire at the end of the month and boss Darren Moore is looking to reshape his squad on a tight budget.