During the 2020 COVID-19 pandemic, Bhakdi started a YouTube channel proposing that the number of deaths stemming from SARS-CoV-2 infection had been overstated. In November 2020 his account was terminated for violating YouTube's community guidelines.[16]

He has been criticised for his theses on the COVID-19 pandemic; according to Medical Tribune [de], they are considered unscientific by a majority of experts.[17]

The German non-profit Correctiv fact-checked one of Bhakdi's YouTube videos, and found a number of problematic claims, including the claim that any COVID-19 vaccine would be "pointless", and that the virus posed no more threat than influenza.[20] Writing for Foreign Policy, Tyson Barker (Head of DGAP's Technology & Global Affairs Program)[29] described Bhakdi as a prominent example from a "crop of debunked but credentialed so-called experts minting conspiracy theories and undermining fact-based information".[30]