Hospitals consume most of the health systems' financial resources. In Portugal, for instance, public hospitals represent more than half of the National Health Service debt and are decisive in their financial insufficiency. Although profit is not the primary goal of hospitals, it is essential to guarantee their financial sustainability to ensure users' health care and the necessary resources. An analysis of the existing literature shows that researches focus mainly on the hospital's technical efficiency. The literature has paid little or even no attention to the use of composite indicators in hospital benchmarking studies. This study uses the Benefit of Doubt methodology alongside recent data about Portuguese public hospitals (2013–2017) to understand the factors that contribute to low performance and high indebtedness levels. Our results suggest that hospitals perform better in terms of access (average score: 0.982). The group of criteria with the lowest performance was efficiency and productivity (average score: 0.919), suggesting resources waste. Financial performance is, in general, higher than quality, raising social concerns about the way that public hospitals have been managed. Findings bring relevant implications. For example, the way hospitals are currently financed should consider efficiency, productivity, quality, and access. Regulators should ensure that minimum performance levels are fulfilled, applying preventive and corrective measures to avoid future low-performance levels. We suggest that hospital managers introduce satisfaction inquiries to improve quality. These improvements can attract more patients in the medium- or long-term; thus, our results are useful to citizens to make a better choice.