Long-term care (LTC) facilities have shown remarkably high mortality rates during the coronavirus disease 2019 (COVID-19) outbreak in many countries1, and different risk factors for mortality have been identified in this setting2–5. Using facilities as the unit of analysis, we investigated multiple variables covering facility characteristics and socioeconomic characteristics of the geographic location to identify risk factors for excess mortality from a comprehensive perspective. Furthermore, we used a clustering approach to detect patterns in datasets and generate hypotheses regarding potential relationships between types of nursing homes and mortality trends. Our retrospective analysis included 167 nursing homes providing LTC to 8,716 residents during the COVID-19 outbreak in Catalonia (northeast Spain). According to multiple regression analysis, COVID-19-related and overall mortality at the facility level were significantly associated with a higher percentage of patients with complex diseases, lower scores on pandemic preparedness measures and higher population incidence of COVID-19 in the surrounding population. When grouping nursing homes into eight clusters based on common features, we found higher mortality rates in four clusters, mainly characterized by a higher proportion of residents with complex chronic conditions or advanced diseases, lower scores on pandemic preparedness, being located in rural areas and larger capacity, respectively.