We present at a national-scale estimates of spatial covariance between areas important for ecosystem services (ES) and biodiversity, at a fixed spatial scale in France. We calculated different diversity and community metrics for common bird communities: taxonomic diversity (TD), functional diversity (FD), community specialization index (CSI), trophic index (TI), phylogenetic diversity (PD) and community evolutionary distinctiveness (CED). The ES multifunctionality (ESMF) was measured using a combination of ES evenness and overall ES estimator. Spatially explicit tests were used to compare the spatial patterns of ES and diversity metrics. Mixed models were used for comparisons. We found low spatial congruence between ES and both diversity and community metrics in France. However, we detected even opposite associations between ES and each biodiversity component. Crop production was negatively associated with CED, it was positively correlated with CSI. No positive associations were found between ESMF and any diversity metric, independently of farming systems. The only significant association was negative: lower values of CED were associated with hotspots of ESMF. We found also a negative effect of crop production on bird CED. The conservation implication is remarkable, because conservation policies focusing solely on the economic value of ES will fail to protect overall biodiversity.