Prior to the onset of the COVID-19 pandemic, the Clausura tournament was scheduled to be played in a similar way to the Apertura, with reversed fixtures, however, its format was altered due to the 5-month suspension of the league.
Since the Apertura winners also ended up in the top two of the aggregate table, they were given a bye to the final and only one semi-final was played by the other two playoff qualifiers.
If teams were tied in points after the two legs of the final, extra time and a penalty shootout would have been played to decide the national champion.
It was also announced that all the remaining matches of the season would be relocated to Lima to avoid the constant travel between cities that clubs must do under normal circumstances, as well as an alteration to the competition format.
[69] On 5 August nine positive cases of COVID-19 were confirmed in Binacional, following the application of tests ordered by the FPF after some players of said club breached the biosecurity protocol upon their arrival to Lima.
[70] In response to this finding the FPF's Medical Commission recommended the isolation of the entire Binacional delegation, meaning that their match against Alianza Lima scheduled for 9 August would not be played.
On 28 November 2020, Alianza Lima were relegated to Liga 2 following a 2–0 loss to Sport Huancayo on the last matchday of the season, however, prior to this event the club's board had requested to the FPF the application of a two-point deduction on Carlos Stein for failing to comply with economic regulations.
Since the FPF initially ruled that Carlos Stein would only get fined, Alianza Lima lodged an appeal to the Court of Arbitration for Sport (CAS).
After months without a final decision and with the 2021 season already underway, on 17 March 2021 the CAS ruled in favor of Alianza Lima and deducted two points from Carlos Stein in the 2020 season's aggregate table, thus reinstating Alianza Lima in the top tier while Carlos Stein ended up relegated.