Bolton have been given a five-point deduction, suspended for 18 months, for failing to fulfil fixtures against Brentford last season and Doncaster this term.
Wanderers were due to play the Bees on 27 April but players refused to play the fixture over unpaid wages.
The club postponed their game against Doncaster on 20 August over welfare concerns for youth players.
A 12-point deduction was already given for entering administration in May.
Following a hearing on 14 November, a disciplinary commission also ruled that Bolton will be handed a financial penalty of £20,000 for the Brentford fixture and £50,000 for the Doncaster game, with half of both fines also suspended for 18 months.
Bolton, who are bottom of League One, pleaded guilty to the charges.
Their fixture against Brentford, which was their final home game and penultimate game of the 2018-19 campaign, was called off 16 hours before kick-off and was initially rearranged for 7 May.
However the game was called off altogether, with the Bees awarded three points for a 1-0 win, while the English Football League said the club were guilty of misconduct.
Their game against Doncaster was called off by the club without the knowledge of Rovers or the EFL, with Wanderers having fielded just three senior outfield players in their heavy defeat at Tranmere just three days before.
Of the suspended five-point deduction, two were handed for the Brentford fixture while three were docked for the Doncaster game, which will be rescheduled and a date confirmed "as soon as possible".
"We acknowledge the decision made by the panel and are pleased that these matters, which occurred under the previous administrations of the club, have now been resolved," Bolton Wanderers chairman Sharon Brittan said.
"Our collective attention must now be fully focused on [manager] Keith Hill, his staff and players as we look to get as many points as we can to climb the League One table.
"Bolton Wanderers supporters and staff have shown tremendous patience and passion throughout and we are now looking forward to working together to continue the rebuilding of this great football club."
Saturday's win against MK Dons moved Wanderers into positive points for the first time this season, having started on -12 points.