After the outbreak of the COVID-19 pandemic in the country, Mutafchiyski was appointed Chairman of the National Crisis Management Staff on 24 February 2020. The general started holding daily briefings where he read out statistical updates and took questions from reporters. He quickly became popular and was arguably the public figure most closely associated with the fight against the pandemic in the country. As early as 13 March 2020, he stated "The key word for all measures is social distancing and self-isolation". and was highly praised for refusing to report discriminatory ethnic statistics against the
Roma minority of Bulgarian citizens. During the summer of 2020, Mutafchiyski formally remained chairman of the National Crisis Management Staff, but was de facto relegated to a more peripheral role, with new Health Minister
Kostadin Angelov starting to lead the daily briefings and sessions on the COVID-19 situation in the country. The general's brash speaking style and clashes with journalists are believed to have contributed to eroding his public image among a number of Bulgarians. In a December 2021 interview, Mutafchiyski stated that Bulgaria had pursued a
COVID-Zero rather than a "living with COVID" strategy until 13 May 2020. The country was very strongly affected by a second wave in the autumn of 2020 and a third one in the spring of 2021. Mutafchiyski has been lauded for being one of the few public figures who remained consistent in demanding the adoption of an uncompromising approach to the virus, refusing to downplay the seriousness of the epidemiological situation in the country, though his position is believed to have ultimately become a minority view within the National Operational Headquarters, which was disbanded in mid April 2021, as well as among many politicians. He has, however, also been criticized himself for bowing down to political pressure and reneging on certain medical principles as well as for playing a part in the decision adopted by Bulgaria not to make full use of its initial EU vaccine quota. == Military missions ==