To retrospectively assess the impact of regular yearly administration of recombinant influenza and single administration of pneumococcal conjugate vaccines on the occurrence of serious respiratory infection including COVID-19 in patients with type 2 diabetes mellitus. Hundred patients with type 2 diabetes mellitus were given Vaxigrip and Prevnar13 vaccines and were evaluated by comprehensive clinical review, airflow screening questionnaire, and routine laboratory investigations with follow-up during the COVID-19 pandemic and compared to a control group of diabetic patients with the same inclusion criteria (n = 100). After Vaxigrip and Prevnar13, there is a significant improvement in respiratory symptoms and a decrease in the airflow screening questionnaire (p = 0.0001) with a significant improvement in inflammatory parameters as neutrophil-lymphocyte ratio, ESR, CRP, and platelet count. Four patients had mild COVID-19 (4%), mainly gastrointestinal with no complications. Twenty-one out of 32 (65.6%) patients in the control group had severe COVID-19. The hazard ratios of significant respiratory tract infection and death due to COVID-19 were 2.29 and 10.24 in the non-vaccinated control (p = 0.001).The severity of COVID-19 in diabetes correlated with HBA1C (p = 0.007), combined Vaxigrip and Prevnar13 vaccination (p = 0.0001), serum creatinine (p = 0.001), neutrophil-lymphocyte ratio (p = 0.001), and thrombocytopenia (p = 0.003). The present study suggested that the combination of Prevnar13 and Vaxigrip may be related to decreased occurrence of serious respiratory infections including COVID-19. Further randomized control trials may be needed to establish a direct causation between the two and clarify these associations.