Since the F₅ (2005), three winter wheat composite cross populations (CCPs) based on germplasm specifically suitable for low-input conditions were subjected to natural selection under organic and conventional management. In the F₆, each CCP was divided into two parallel populations (12 CCPs in total) and maintained continuously until 2018. Commonly used modern cultivars with different disease susceptibilities were grown alongside to assess the agronomic performance of the CCPs. The organically managed CCPs were comparable in yield and foliar disease resistance to two continuously used reference cultivars, Achat and Capo. In contrast, under conventional management the cv. Capo outyielded the CCPs (Achat was not tested), highlighting the importance of parental cultivar choice for specific management systems. The CCPs were found to be moderately resistant to brown rust and even to the newly emerged stripe rust races prevalent in Europe since 2011. Differences between the CCPs were mainly due to parental genetic background and were significant in the first five generations, but were no longer so in the last five generations. In addition, these differences tended to vary depending on the experimental year and the environmental stresses present. In conclusion, the CCPs despite being derived from older cultivars are able to compete with more recently released reference cultivars under organic farming practices and represent a dynamic germplasm resource.