We aimed to study the impact of the COVID-19 pandemic on exclusive breastfeeding (EBF) rate and routine follow-up practices including immunization. A total of 62 neonates born to COVID-19 positive mothers and an equal number of neonates born to COVID-19 negative mothers were prospectively evaluated for EBF rate and routine neonatal follow-up practices including delay (>7 days) in routine immunization at 3 months follow-up. We further tried to compare the results across two epochs (epoch 1, March-June 2020 and epoch 2, July-November 2020). There was significantly lesser number of babies born to COVID-19 positive mothers on EBF at 3 months of age when compared with the control group (45.1% vs. 96.7%, p = 0.00) as well it was significantly lesser in epoch 1 when compared with epoch 2 (16% vs. 74%, p = 0.00). Further, a significantly higher number of babies born to COVID-19 positive mothers had their routine immunization delayed with no significant difference across the epochs. There was no significant difference in growth parameters between babies born to COVID-19 positive mother when compared with the control group as well as across the epochs. The COVID-19 pandemic has significantly disrupted the EBF rates as well as hampered the routine immunization practices among babies born to COVID-19 positive mothers. Although such practices got improved after the implementation of evidence-based national guidelines, but it is still much below when compared with those born to COVID-19 negative mother.