Protein degradability in forage legumes is of global importance because utilization efficiency of forage has economic and environmental consequences. However, there are no published studies on the effect of legume stand structure on differences in crude protein (CP) fractions. The main objective of the present research was therefore to investigate differences in CP fractions in leaves and stems of lucerne (Medicago sativa L.) during the growing season. Stand traits were measured over 2 years, and forage was sampled at the early bud and early flower stages in the first, second and third cuts. Stems had significantly higher concentrations (in g kg−1 CP) of non‐protein (fraction A: 430 g kg−1 CP) and indigestible nitrogen (fraction C: 92 g kg−1 CP) than leaves and had lower relative content of true protein (fraction B: 478 g kg−1 CP). In the total forage (stems and leaves combined), about 80% of the variation in CP fractions was explained by year, cut and maturity. Year was the most important factor, particularly for the B fractions. Cut was the second‐most important factor; its main effect was that the relative abundance of fraction A declined from 394 g kg−1 CP in the first cut to 293 in g kg−1 CP the third cut. Maturity increased the amounts of indigestible fraction C and protein fractions B1 and B3. This was associated with the leaf weight ratio, which had an inverse relationship with maximal stem length and dry matter yield. Variation partitioning showed that 75% of CP fraction variability associated with cut, maturity and year could be explained by the evaluated stand traits. This research has highlighted the need to consider plant morphological traits when legume CP fractions are evaluated.