Abstract Background The burden of chronic diseases is rapidly rising, both in terms of morbidity and mortality. This burden is disproportionally carried by socially disadvantaged population subgroups. Quality-adjusted life years (QALYs) measure the impact of disease on mortality and morbidity into a single index. This study aims to estimate the burden of chronic diseases in terms of QALY losses and to model its social distribution for the general population. Methods The Belgian Health Interview Survey 2013 and 2018 provided data on self-reported chronic conditions for a nationally representative sample. The annual QALY loss per 100,000 individuals was calculated for each condition, incorporating disease prevalence and health-related quality of life (HRQoL) data (EQ-5D-5L). Socioeconomic inequalities, based on respondents’ socioeconomic status (SES), were assessed by estimating population attributable fractions (PAF). Results For both years, the largest QALY losses were observed in dorsopathies, arthropathies, hypertension/high cholesterol, and genitourinary problems. QALY losses were larger in women and in older individuals. Individuals with high SES had consistently lower QALY loss when facing a chronic disease compared to those with low SES. In both years, a higher PAF was found in individuals with hip fracture and stroke. In 2013, the health inequality gap amounts to 33,731 QALYs and further expanded to 42,273 QALYs in 2018. Conclusion Given that chronic diseases will rise in the next decades, addressing its burden is necessary, particularly among the most vulnerable (i.e. older persons, women, low SES). Interventions in these target groups should get priority in order to reduce the burden of chronic diseases.