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Objectives We aim to compare differences in mortality risk factors between admission and follow-up incorporated models. Methods A retrospective cohort study with 524 patients with confirmed COVID-19 infection admitted to a tertiary medical center in São Paulo, Brazil, from March 13 th to April 30 th , 2020. We collected data at admission, 3 rd , 8 th and 14 th day of hospitalization. We calculated the hazard ratio (HR) and compared 28-day in-hospital mortality risk factors between admission and follow-up models using a time-dependent Cox regression model. Results Of 524 patients, 50.4% needed mechanical ventilation. The 28-day mortality rate was 32.8%. Compared to follow-up, admission models under-estimated the mortality HR for peripheral oxygen saturation<92% (1.21 versus 2.09), heart rate>100bpm (1.19 versus 2.04), respiratory rate>24ipm (1.01 versus 1.82) and mechanical ventilation (1.92 versus 12.93). Low oxygen saturation, higher oxygen support and more biomarkers including lactate dehydrogenase, c-reactive protein, neutrophil-lymphocyte ratio and urea remained associated with mortality after adjustment for clinical factors at follow-up compared to only urea and oxygen support at admission. Conclusions The inclusion of follow-up measurements changed mortality hazards of clinical signs and biomarkers. Low oxygen saturation, higher oxygen support, lactate dehydrogenase, c-reactive protein, neutrophil-lymphocyte ratio and urea could help prognose patients during follow-up.