On 30 August 2019, Illarramendi suffered a broken fibula in a Basque derby match against Athletic Bilbao; it was presumed the injury would keep him out for a few months, but it was found he required surgery to his shin and ankle ligaments, and he did not feature again prior to the season being halted in March 2020 due to the COVID-19 pandemic in Spain. The delay seemed to have given him time to return before its conclusion, but in June 2020 he suffered a further muscle injury on the training ground, and made no further appearances.