Abstract Empirical evidence on Europe integration indicates a process of convergence between countries, but not within regions. We aim to assess the relationship between spatial and social inequalities in the EU regions for the 2000–2016 period. Our results revise existing evidence about the evolution of some descriptive measures of inequality, showing that: (i) inequalities exist at the regional level with a growing disconnection between the geography of production that becomes more unequal, as do the geography of incomes; (ii) when analyzing the positive relationship between the growth of regional inequalities and the gross domestic product (GDP), a trade-off between spatial equity and growth seems possible. Our econometric results indicate that inequalities persist and create a type of path dependence, correlated to proximity in space. Spatial inequalities in the GDP strongly affect interpersonal inequalities. The per capita expenditure on social transfer negatively affects social inequalities; however national redistribution only mitigates the impact of spatial inequalities without compensating them completely. Other variables of spatial inequality such as the unemployment rates’ regional dispersion in each country and the geographic concentration of economic activity (i.e., the effects of agglomeration on social inequalities) are significant. Thus, more agglomeration, which increasing returns of scale in production induce, increases inequalities.