Perinatal transmission of COVID-19 is poorly understood and many neonatal intensive care units' (NICU) policies minimize mother-infant contact to prevent transmission. We present our unit's approach and ways it may impact neonatal microbiome acquisition. We attended COVID-19 positive mothers' deliveries from March-August 2020. Delayed cord clamping and skin-to-skin were avoided and infants were admitted to the NICU. No parents' visits were allowed and discharge was arranged with COVID-19 negative family members. Maternal breast milk was restricted in the NICU. All twenty-one infants tested negative at 24 and 48 hours and had average hospital stays of nine days. 40% of mothers expressed breastmilk and 60% of infants were discharged with COVID-19 negative caregivers. Extended hospital stays, no skin-to-skin contact, limited maternal milk use, and discharge to caregivers outside primary residences, potentially affect the neonatal microbiome. Future studies are warranted to explore how ours and other centers' similar policies influence this outcome.