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Healthcare workers (HCWs) face an unprecedented higher risk of COVID-19 infection due to their work and exposure. In this study, we aim to examine the associated risk factors for COVID-19 infection among HCWs in North-East Nigeria. We used data collected retrospectively among a cohort of clinical and non-clinical HCWs in six healthcare facilities in Adamawa State, Nigeria. We estimated the marginal probability of COVID-19 infection among HWCs using alternating logistic regression via the generalized estimating equations (GEE) approach. Among the 318 HCWs, 178 (55.97%) were males, mean (±SD) age was 36.81 (±8.98), 237 (74.76%) were clinical, and 80 (25.24) were non-clinical staff. The overall prevalence of COVID-19 was 16.67% among HCWs. After adjusting for other variables in the model, our results showed that clinical staff had a 5-fold higher risk of COVID-19 infection than non-clinical staff (aOR = 5.07, 95% CI: 1.32-19.52). Moreover, significant exposure risk factors for COVID-19 infection for HCWs increase with age, time spent attending to patients, caring for COVID-19 patients, and having worked with COVID-19 samples, while the risk decreases with the use of an N95 mask. Our findings suggested that the burden of COVID-19 infection is higher for clinical staff than non-clinical staff, and increasing age contributed to the increased risk.