Autologous blood transfusion is known to have advantages over allogeneic transfusion. The COVID-19 pandemic intensified the already existing shortage of allogeneic blood supply. We carried out a study during this period with the aim to elicit the effects of autologous blood collection and transfusion, to compare the peri-operative outcomes of autologous and allogeneic transfusion practices and also to assess the influence of the autologous transfusion programme in the Blood Centre inventory. It was prospective observational comparative study among neurosurgical and vascular surgical patients in a tertiary care centre in South India. 141 patients were allocated into Group I (n = 71) who received autologous transfusion and those who received conventional allogeneic transfusion were clustered as Group II (n = 72) for analysis. We employed Acute Normovolemic Hemodilution (ANH), Pre-deposit Autologous Donation (PAD) and Intra-operative Cell Salvage (ICS) as various modalities for autologous blood collection. In our study, 43 (60.6%) from Group I received exclusive autologous blood transfusion, whereas 28 (39.4%) required additional allogeneic transfusion. No significant difference in hemoglobin, hematocrit, platelet count and INR were observed between the groups post transfusion. Significant difference was observed in the thoracoabdominal aortic aneurysm (TAAA) patients with respect to duration of ICU stay (2.7 ± 1.1 days in Group I and 6.2 ± 0.8 days in Group II; p = 0.002) and re-exploration due to bleeding (16.7% in Group I and 40% in Group II; p = 0.048). Autologous blood transfusion is safe and effective. It can be employed as routine practice and also during any acute shortage or pandemic.