Nitrogen (N) is considered quantitatively most important for crop growth and productivity. The improvement of crop N use efficiency is economically beneficial to farmers and reduces the negative environmental impact of agriculture. Root traits are promising, yet underexploited breeding targets to improve N use efficiency. We aimed to evaluate (1) the effects of genotype and environment on N use efficiency and various root architectural and anatomical traits; and (2) the relationships between root traits, N uptake and conversion efficiency. Nine spring wheat genotypes were grown on compacted and non-compacted soil during two years with contrasting weather conditions in Central Sweden. Wheat genotype and year caused considerable variation in several root and N use efficiency traits. Negative correlations were found between N uptake efficiency and N conversion efficiency; root number and diameter; root number and angle; and metaxylem number and diameter. The N uptake efficiency increased with shallower root angle, higher root number, smaller root diameter, higher metaxylem number and smaller metaxylem diameter; whilst N conversion efficiency showed the opposite pattern. We conclude that a negative relationship observed between N uptake efficiency and N conversion efficiency can be linked to trade-offs between embryonic root traits.