The severe acute respiratory syndrome coronavirus disease-2 (SARS-CoV-2) pandemic of 2020-2021 created unprecedented challenges for clinicians in critical care transport (CCT). These CCT services had to rapidly adjust their clinical approaches to evolving patient demographics, a preponderance of respiratory failure, and transport utilization stratagem. Organizations had to develop and implement new protocols and guidelines in rapid succession, often without the education and training that would have been involved pre-coronavirus disease 2019 (COVID-19). These changes were complicated by the need to protect crew members as well as to optimize patient care. Clinical initiatives included developing an awake proning transport protocol and a protocol to transport intubated proned patients. One service developed a protocol for helmet ventilation to minimize aerosolization risks for patients on noninvasive positive pressure ventilation (NIPPV). While these clinical protocols were developed specifically for COVID-19, the growth in practice will enhance the care of patients with other causes of respiratory failure. Additionally, these processes will apply to future respiratory epidemics and pandemics.