Few studies have assessed the impact of the COVID-19 pandemic on non-COVID diseases and healthcare quality. We aimed to evaluate changes in rates of hospitalisations, complications, in-hospital mortality, and readmissions among patients with non-COVID diseases during a one-year period after the pandemic onset. From March 2018 to February 2021 a retrospective observational study of hospital admissions in a university hospital in Spain was conducted. Non-COVID hospitalisations admitted through the emergency department were compared between the pre-COVID period (n = 28,622) and the COVID period (n = 11,904). We assessed rate ratios (RaR), comparing the weekly number of admissions and risk ratios (RR) to examine rates of complications, in-hospital mortality, readmissions, and severity. Statistical significance was set at p < 0.05. The weekly admission rate dropped by 20.8% during the complete lockdown. We observed significant reductions in admissions related to diseases of the respiratory system and circulatory system. Admissions for endocrine and metabolic diseases increased. The complication rates increased (RR = 1.21, 95% CI: 1.05;1.4), while in-hospital mortality rates held steady during the COVID period (RR = 1.09, 95% CI: 0.98;1.2). Hospital efforts to maintain quality and safety standards despite disruptions translated into a moderate increase in complications but not in in-hospital mortality. Reduced hospitalisations for conditions requiring timely treatment may have significant public health consequences.