The circumstances into which individuals are born can place fundamental constraints on their future economic opportunities1–5, leading to a mismatch between talent, education and occupation. One major determinant of this inequality of opportunity is the absence of intergenerational educational mobility2. Here we extend existing knowledge on intergenerational mobility by presenting The European Atlas of Spatially Disaggregated Intergenerational Mobility (EUROPE-IGM-ATLAS), a panel database comprising indicators of intergenerational mobility for European subnational regions. In doing so, we make two contributions. First, we extend existing knowledge on the development of intergenerational mobility in European regions. The EUROPE-IGM-ATLAS reveals several spatiotemporal trends that characterize the changing geography of opportunity in Europe. For example, we show that observed increases in intergenerational mobility primarily stem from improvements in educational achievements among individuals from families at the lower end of the educational distribution, with fewer changes in rank across the educational spectrum. However, these increases are not uniformly distributed. Regions with a high degree of educational inequality also exhibit lower levels of intergenerational mobility, implying the co-existence of inequality both within and between generations. Second, we use this database to provide evidence on the relationship between intergenerational mobility and innovation. We provide large-scale time-series evidence that European regions with higher intergenerational mobility achieve higher innovation outcomes, one important driver of economic growth. Subsets of results further indicate that this relationship is nonlinear and that distinct mechanisms operate in major innovation hubs.