Introduction: Recent pandemic of COVID-19 has shaped economic, social, and political aspects of human civilization. Pregnant women were also affected during the pandemic. Effect of COVID-19 infection on pregnancy outcome as the pandemic progressed through various phases (first, second, and third waves) is of importance. Methodology: A cross-sectional study carried out in a dedicated COVID tertiary care maternity unit during three waves of pandemic. Around 405 pregnant women with active COVID-19 infection at the time of delivery giving birth to 411 newborns (6 cases of twins) were enrolled to study the perinatal outcome. Primary outcome of study was to analyze the perinatal outcome in COVID-19-affected pregnant women and secondary outcome of study was to understand the sociodemographic profile of women affected by COVID-19 and to compare the maternal and fetal affection in all three phases of the COVID-19 pandemic. Results: Among three phases, most commonly affected age-group was 21–25 years (44.2%). Among the affected women, body mass index (BMI) was normal in 49.9% of women. Phase-wise affection did not show any statistical difference for maternal age, BMI, socioeconomic class, parity, and gestational age. Overall 48.6% of women were symptomatic. Symptomatology and high dependency unit (HDU)/intensive care unit (ICU) requirement showed statistical significant difference in three waves of pandemic (p < 0.001). The second wave had severe affection than the first and third waves. All four (1%) maternal mortalities during study period were noted in the second wave. Commonest obstetric high risks noted were anemia, 34.6% cases, followed by previous lower segment cesarean section (LSCS), 27.2% cases, and preeclampsia, 18.8% cases. Preterm delivery rate was found to be 27.4%. Obstetric high risks and preterm delivery rate did not show any statistical difference in all three phases of COVID. Cesarean section rate was 48.1% in COVID-19 pregnant population. Cesarean section rate among three phases showed statistical significance with highest (54.7%) in the first wave of COVID-19 pandemic. Neonatal transmission rate was 1.02% in our study. Stillbirth rate and neonatal intensive care unit (NICU) admission did not show any statistical difference in three waves of COVID-19 infection. Conclusion: The second wave of COVID-19 was more severe compared with first and third waves with more symptomatic cases requiring HDU/ICU admission and high maternal mortality. Neonatal outcome did not show statistical difference in three stages of COVID-19 pandemic.