Highlights •This is the first study documenting systems effects on the evolution of the composite cross populations (CCP).•Characteristics for early vigour, but not allelopathy, were improved after 5 years in organically-managed CC populations.•Evolutionarily, parallel CCPs demonstrated very similar behaviour indicating that the differences are related to individual populations and management systems.•Evolutionary changes towards early vigour in the organic CCPs are probably selection for higher nitrogen uptake increased competition for light and larger seeds.•Hydroponics and bioassays techniques offer an additional highly sensitive way to study early vigour and allelopathy under controlled conditions.