The Coronavirus 2019 (COVID-19) pandemic has dramatically increased the frequency of mask-wearing in the general population and has created challenges during ophthalmic examination. During examination, lenses utilized during slit lamp examination have been noted to fog significantly from the patient’s own respirations leaving the superior part of mask. This is supported by recent literature, which demonstrated increased jet airflow leaving the superior portion of the mask directed towards the periorbita and ocular surface. Furthermore, numerous ophthalmologists have proposed the potential for an increased risk of ocular infection, notably during procedures in which the mask is kept in place but inadequately sealed, despite standard pre procedure prepping and precautions. This raises the question, does frequent mask-wearing during the COVID-19 pandemic alter the ocular surface microbiome? This topic was investigated using 16S sequencing to determine the relative abundance of each bacteria comprising the microbiome of the conjunctiva. Statistically significant results demonstrated shifts in the ocular flora from known biomes correlating with length of mask wear. This change necessitates changing practice patterns associated with the sterile prep and antibiotic regimens associated with routine facial procedures and surgeries. It further prompts investigation and review of antibiotics utilized for routine ocular and facial infections. In doing this research, we further our understanding of the ocular surface microbial community during the COVID-19 pandemic and encourage further investigation into ways COVID-19 may be impacting ophthalmic disease and its lasting impacts on military readiness.