Background Blood transfusion has been associated with a high risk of transfusion-transmissible infections (TTIs). These infections pose great threats to the availability and safety of blood supply for transfusion, particularly in sub-Saharan Africa (SSA) where the burden of disease is alarmingly high. We describe the incidence and determinants of TTIs to help target interventions for safety and increased access to safe blood. Methods This was secondary data analysis of a cohort of blood donors from the Malawi Blood Transfusion Service (MBTS) who donated blood from 2005–2015. Incidence was obtained by dividing the number of new cases by the total person-years at risk and survival probabilities computed by Kaplan-Meier estimates. Logistic regressions were used for risk factors. Results We analysed data from 47,075 registered blood donors of which the majority were male (84%) with a median age of 22 years (IQR=18–22). Of the registered donors, 3,439 (7.31%) were infected with at least one TTI (HIV, HCV or HBV). HBV was the most common TTI with 2.63% (n=1,238), followed by HIV with 1.74% (n=818) and HCV with 1.28% (n=602). Overall, TTI incidence was 43.4 per 10,000. Donors aged 20–24 (OR= 2.15, 95% CI= 1.35–3.40), and 30–34 (OR= 2.68, 95% CI= 1.67–4.32), males (OR= 1.65; 95% CI= 1.47–1.85), and married donors (OR= 1.93; 95% CI= 1.38–2.69) had significantly higher odds of TTI in the multivariate logistic model. Infection with syphilis was a common significant risk factor for incident HIV (OR= 2.62, 95% CI= 1.57–4.38), HCV (OR= 2.03, 95% CI= 1.04–3.98), and HBV (OR= 1.71, 95% CI= 1.01–2.89). Conclusion The overall incidence of TTIs in the Malawian donor population is comparatively low. The incidence of HIV, HCV and HBV is high in males, the unemployed, donors living in the Central Region, involved in high-risk sexual behaviour, and co-infected with syphilis. HBV is most common among supposedly healthy donors, followed by HIV and HCV. TTI therefore, remains a cause for concern toward availability and safe blood supply. Implementation of strict and proper donor selection criteria and continuous screening for TTI indicators can help maximise safe blood supply and transfusion.