Background: COVID-19 rapidly spread around the world, putting health systems under unprecedented pressure and continuous adaptations. Well-established health information systems (HIS) are crucial in providing data to allow evidence-based policymaking and public health interventions in the pandemic response. This study aimed to compare morbidity information between two databases for COVID-19 management in Portugal and identify potential complementarities. Methods: This is an observational study using records from both COVID-19 cases surveillance (National Epidemiological Surveillance System; SINAVE) and related deaths (National e-Death Certificates Information System; SICO) systems, which were matched on sex, age, municipality of residence and date of death. After the linkage, morbidity reported in SINAVE and identified in SICO, through the application of Charlson and Elixhauser comorbidity indexes algorithms, were compared to evaluate agreement level. Results: Overall, 2285 matched cases were analyzed, including 53.9% males with a median age of 84 years. According to the method of data reporting assessment, the presence of any morbidity ranged between 26.3% and 62.5%. The reporting of ten morbidities could be compared between the information reported in SINAVE and SICO databases. The proportion of simultaneous reporting in both databases ranged between 5.7% for diabetes and 0.0% for human immunodeficiency virus infection or coagulopathy. Minimal or no agreement was found when assessing the similarity of the morbidity reporting in both databases, with neoplasms showing the highest level of agreement (0.352, 95% IC: 0.277–0.428; p < 0.001). Conclusion: Different information about reported morbidity could be found in two HIS used to monitor COVID-19 cases and related deaths, as data are independently collected. These results show that the interoperability of SICO and SINAVE databases would potentially improve available HIS and improve available information to decision-making and address COVID-19 pandemic management.