Introduction Quaternary ammonium compounds (QACs) are the active ingredient in the majority of disinfectants approved for use against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the coronavirus disease 2019 (COVID-19). Although widely used, they have been linked to infertility and birth defects in animals, and have been shown to increase proinflammatory cytokines, decrease mitochondrial function, and disrupt sterol biosynthetic pathways in a dose-dependent manner in humans. This study examined if there was an increased use of QAC-based disinfectants among healthcare settings in response to the COVID-19 pandemic and aims to bring to light the negative health outcomes that this rise in QAC exposure may pose.  Methods This hypothesis was explored using a telephone survey tool with both open-ended and closed-ended questions to assess changes in disinfection practices within hospitals, private practices, and dental practices. To ensure that the data were most representative of the United States, all states were ranked based on 28 health metrics tracked by the Kaiser Family Foundation. Those that ranked closest to the national average were Arizona, Florida, Illinois, Michigan, Pennsylvania, and Virginia. Healthcare facilities within these states were called at random and asked about changes in disinfection practices, specifically regarding the disinfectant type, product concentration, changes in the frequency of cleaning, and changes in the cleaning method. Additional data such as demographics, hospital ward type, and practice type were also obtained. Results QAC-based disinfectants were one of the most commonly used products in the surveyed hospitals, private practices, and dental practices both before and throughout the pandemic. Among all the medical facilities surveyed, approximately 80 to 90% indicated an increase in the frequency of cleaning. Within private practices, approximately 80 to 90% increased both spraying and wiping, while within dental practices, 75% increased wiping and only 60% increased spraying. Over 80% of hospitals reported an increase in all methods of disinfection within each ward type. The number of dental practices using QAC-containing disinfectants increased due to the pandemic. In hospitals, the class of disinfectant varied considerably by ward, but overall fewer of them used QAC-based disinfectants and more relied on peroxide-containing disinfectants. Conclusions This study identified increases in the disinfection frequency and changes to disinfection products within healthcare settings as a result of the COVID-19 pandemic. The predominant use of QAC-based products and the increased frequency of disinfection are important findings as they indicate heightened exposure. Emerging literature has identified adverse health outcomes in both animals and humans from contact with QACs. Increased disinfection during a pandemic or disease outbreak is critical to control the spread of disease; however, further research is needed to investigate whether the use of QAC-containing disinfectants to combat COVID-19 results in unintended disease burden in the healthcare workers.