Seattle Sounders will play Columbus Crew in the MLS Cup final after winning the Western Conference finals on Monday
Major League Soccer lost almost $1bn (£750m) in revenue during 2020 because of the coronavirus pandemic.
MLS was only two weeks into its historic 25th season when a halt was called to the campaign in March.
It did not resume until July, with the MLS is Back competition in Florida, before a revised regular schedule ran from 12 August.
“The overall [financial] impact is going to be deeper than we expected,” said MLS commissioner Don Garber.
With the three Canadian teams forced to play all their matches in the United States and Columbus Crew only able to admit a crowd of 1,500 when they host Seattle Sounders in the MLS Cup final on Sunday, the financial effects of the season will be felt for a long time.
“Revenue for the league and its clubs is down almost $1bn compared to last year,” added Garber.
“But we also incurred expenses we were not intending to occur, including charter planes for the teams and creating the whole bubble around MLS is Back.”
It has led to a difficult first season for the two expansion teams, David Beckham’s Inter Miami and Nashville, who made the Eastern Conference semi-finals, and creates an uncertain backdrop for Austin FC, who will enter the league in 2021.
However, while plans continue around a March launch for the next season, huge uncertainty remains.
“We are concerned about the situation leading into 2021 and we are trying to figure out how to manage through it,” said Garber. “No business could sustain the kind of impact we sustained for two years in a row.
“The challenge for next season is nobody has the magic date for when fans can enter stadiums and it will vary state by state.
“We need to make a schedule. We can’t wait for a vaccine and we don’t know what the reaction will be of fans returning to stadiums.
“It is not just about fans. Fifa has laid out their international dates and Concacaf has laid out Champions League dates. We will need flexibility.”