MLS resumed with a special tournament in July hosted in the Orlando area, and teams returned home a month later to play in matches behind closed doors.

[7] The team finished the 2019 season with the second-best record in the Western Conference and won their second MLS Cup title after defeating Toronto FC at CenturyLink Field.

General manager Garth Lagerwey stated that the club had yet to make major roster decisions due to the ongoing negotiations between the league and the MLS Players Association over a new collective bargaining agreement, which would affect the salary cap.

[14] The club also signed defenders Yeimar Gómez Andrade, Miguel Ibarra, and Shane O'Neill to replace Torres, Kee-hee, and left-back Brad Smith, who returned to AFC Bournemouth following the end of his loan.

[26] In Mexico City, the Sounders played two friendlies on February 12 against local teams, drawing 2–2 with Atlético Zacatepec using most of their starting lineup and defeating the under-20 reserves for UNAM Pumas 2–1.

[40] A stadium concessions worker tested positive for COVID-19 after a Seattle Sea Dragons game, but public health authorities permitted the Sounders match to be held with full capacity.

[38][41] The club remained in contact with local health officials over the following week and prepared several contingency plans to address the COVID-19 outbreak, including postponement or playing without spectators.

[50] Sounders majority owner Adrian Hanauer also announced a $500,000 investment into a club relief fund for businesses, workers, and non-profits in Seattle that were affected by the lack of matches at CenturyLink Field.

[53] The Sounders resumed individualized training sessions at Starfire Sports on May 18 with outdoor social distancing, limited use of indoor facilities, daily temperature and symptom screenings, and use of personal protective equipment.

[61][62] A rising number of positive COVID-19 cases in Florida and among MLS players prompted the Emerald City Supporters to organize a small protest at the final Sounders training session before their flight to join the tournament.

[78][79] The Cascadia Cup, contested by the Sounders alongside rivals Portland and Vancouver, was not awarded during the 2020 season following a decision by supporters groups to exclude matches without fans in attendance.

[80][81] The club also announced a new broadcast contract with Amazon to simulcast locally televised matches on their Prime Video platform for residents of Washington state; the streaming deal had been negotiated in March, but its implementation was delayed due to the COVID-19 pandemic.

[83] As part of a multi-sport strike by professional athletes in the United States to protest the shooting of Jacob Blake in Wisconsin, the Sounders refused to play against the LA Galaxy.

[85] The Sounders traveled two days later to play Real Salt Lake, who were permitted to admit over 4,000 spectators into Rio Tinto Stadium, and took the lead twice through a penalty scored by Lodeiro and later a ]header by defender Yeimar Gómez Andrade for his first career MLS goal.

The Sounders signed two returning defenders, Brad Smith from free agency and Román Torres in a trade with Inter Miami CF, to add depth and options to rotate players for midweek matches.

[90][91] The team lost 1–0 to the Timbers, who took an early lead through Yimmi Chará; Portland goalkeeper Steve Clark made six saves as the Sounders had a majority of possession and chances in the second half while unsuccessfully searching for an equalizer.

[94] Three players—Ruidíaz, midfielder Gustav Svensson, and defender Xavier Arreaga—were called up to their national teams in October and were expected to miss up to five MLS matches due to a required ten-day quarantine period.

[103] In their fourth meeting of the season, Seattle and Portland played to a 1–1 draw at CenturyLink Field after several missed chances to score were followed by a late goal from Will Bruin in stoppage time.

[104] Several key players, including Ruidíaz and Svensson, returned from national team duty for a match against Vancouver Whitecaps FC that was played at Providence Park in Portland, Oregon, due to travel restrictions imposed at the Canadian border.

[107] Three days later, the Sounders earned a 1–1 draw with the LA Galaxy after Ruidíaz scored in stoppage time; the away fixture replaced the August match that had been postponed due to player protests.

The Sounders finished the 2020 regular season as the second seed in the Western Conference behind Sporting Kansas City, as determined by points per game because teams did not play the same number of matches, and had only one loss at home.

[111] In the fifth match of the season between the two teams, the Sounders took a 1–0 lead at halftime from an early Lodeiro goal; the scoreline was preserved by Stefan Frei, who saved a penalty taken by Carlos Vela to keep a shutout.

[106] The Sounders then hosted the Western Conference Final on December 8 against fourth-seeded Minnesota United FC, who had defeated top-seeded Kansas City in an upset victory four days earlier.

Defender Gustav Svensson, who had missed the first two playoff matches due to a positive COVID-19 test, scored the winning header in stoppage time off a Lodeiro corner kick.

[118] Three Crew players—Darlington Nagbe, Pedro Santos, and Vito Wormgoor—were declared "medically not cleared to play" due to COVID-19, and Sounders defender Xavier Arreaga remained home for the birth of his child.

A play-in round was added for the four lowest-ranked Eastern Conference entrants; the rest of the playoff matches were played between November 21 and December 12 with hosting determined by overall finish on the table.

[138] A base salary cap of $4.9 million applied to the non-supplemental players with exceptions for the club's three designated players—João Paulo, Nicolás Lodeiro, and Raúl Ruidíaz—who each counted for a reduced amount.

[147] Four players made appearances in all 29 of the team's matches: goalkeeper Stefan Frei, defender Nouhou Tolo, midfielder Cristian Roldan, and forward Jordan Morris.

[195] Following the end of the season, the Sounders closed their COVID-19 relief fund after it had raised and distributed $1.1 million in grants to 785 people and 134 businesses affected by the pandemic and lack of fan traffic for home matches.

[199] Jordan Morris was loaned for six months to Welsh side Swansea City AFC in the EFL Championship, but he only played five matches before a second career anterior cruciate ligament injury in February 2021.