The failure of tuberculin as a cure for tuberculosis led to significant criticism of Koch. Some accused him of prematurely announcing the treatment before it had been adequately tested, raising false hopes and causing harm to patients. There were allegations of data manipulation and suppression of negative results.

Koch's relationship with Paul Ehrlich, another prominent scientist at the Institute for Infectious Diseases, was complex and sometimes strained. While Ehrlich admired Koch's scientific achievements, there was also competition and disagreement between them, particularly regarding research priorities and methodologies.

As with many early scientific investigations, some of Koch's experiments involved ethical considerations that might be viewed differently today. For example, the use of animal experiments to demonstrate the pathogenicity of microorganisms raised concerns among animal welfare advocates, even during that time.

In some cases, Koch was criticized for not fully acknowledging the prior work of other scientists. For example, Filippo Pacini had described "Vibrio cholerae" decades before Koch's identification of the bacterium as the causative agent of cholera. However, Koch is credited with definitively proving its role in causing the disease and developing improved methods for isolation and identification.