In Europe, population estimates of breeding birds are produced nationally and are periodically compiled at EU or pan-European scales. Until now, no other source was available to explore the robustness of these estimates. In this study, we compared population sizes reported in the latest edition of the European Red List of Birds (ERLoB) with those produced using data from the second European Breeding Bird Atlas (EBBA2) to assess their consistency and determine parameters behind variability in population estimates that deserve further attention in the future. In general, European population estimates derived from summing local abundance data from EBBA2 were similar to those obtained from ERLoB, although for some species they differed considerably, particularly in those distributed mainly in southern Europe. National population estimates from EBBA2 also did not differ markedly from those in ERLoB. However, we found that EBBA2 provided larger national population sizes than ERLoB for widespread species, suggesting that spatial information is more relevant for properly assessing their population size than for localised species. Our analysis also showed that, in general, population estimates based on robust methodological protocols (e.g. complete counts, statistical inference) contributed to reducing differences between ERLoB and EBBA2 values. Interestingly, EBBA2 and ERLoB estimates were quite similar for species classified in Europe as “Threatened” or “Near Threatened”, whereas the values for “Least Concern” species were consistently different between these two sources. Our results indicate which type of species would benefit from additional efforts to improve national population estimates and their consistency across countries, issues that are of paramount importance for guiding conservation strategies in Europe.