Manager Mikey Harris is considering his future at Salisbury City, BBC Wiltshire has learned.
The 29-year-old is thought to be unhappy with the Conference Premier club's current financial plight.
Salisbury have been under a Football Conference transfer embargo since April and it is thought staff wages have been delayed for the last two months.
The club's new owners have until 17:00 BST on Thursday to pay the salaries or risk being thrown out the league.
Morrocan businessman Outail Touzar and fan Mark Winter took over the Whites last month.
Winter told BBC Wiltshire on Tuesday he was confident the players and staff would receive their money in time.
Salisbury have suffered five years of financial turmoil and previously incurred a double demotion in 2010, after failing to pay back a creditor by a set deadline.
Harris has been at Salisbury for six years and worked as assistant manager under Darrell Clarke when they dropped to the Southern Premier.
The management duo secured two promotions in three years to return to non-league's top flight, before Clarke opted to join Bristol Rovers last summer.
Harris succeeded Clarke as boss, making him English football's youngest full-time manager, and they finished 12th in his first season in charge.