Background: COVID-19 is caused by SARS-CoV-2 infection and has reached pandemic proportions. Since then, several clinical characteristics have been associated with poor outcomes. This study aimed to describe the morbidity profile of COVID-19 deaths in Portugal. Methods: A study was performed including deaths certificated in Portugal with “COVID-19” (ICD-10: U07.1 or U07.2) coded as the underlying cause of death from the National e-Death Certificates Information System between 16 March and 31 December 2020. Comorbidities were derived from ICD-10 codes using the Charlson and Elixhauser indexes. The resident Portuguese population estimates for 2020 were used. Results: The study included 6701 deaths (death rate: 65.1 deaths/100,000 inhabitants), predominantly males (72.1). The male-to-female mortality ratio was 1.1. The male-to-female mortality rate ratio was 1.2; however, within age groups, it varied 5.0–11.4-fold. COVID-19 deaths in Portugal during 2020 occurred mainly in individuals aged 80 years or older, predominantly in public healthcare institutions. Uncomplicated hypertension, uncomplicated diabetes mellitus, congestive heart failure, renal failure, cardiac arrhythmias, dementia, and cerebrovascular disease were observed among COVID-19 deceased patients, with prevalences higher than 10%. A high prevalence of zero morbidities was registered using both the Elixhauser and Charlson comorbidities lists (above 40.2%). Nevertheless, high multimorbidity was also identified at the time of COVID-19 death (about 36.5%). Higher multimorbidity levels were observed in men, increasing with age up to 80 years old. Zero-morbidity prevalence and high multimorbidity prevalences varied throughout the year 2020, seemingly more elevated in the mortality waves’ peaks, suggesting variation according to the degree of disease incidence at a given period. Conclusions: This study provides detailed sociodemographic and clinical information on all certificated deaths from COVID-19 in Portugal during 2020, showing complex and extreme levels of morbidity (zero-morbidity vs. high multimorbidity) dynamics during the first year of the pandemic in Portugal.