Six cropping populations, three variety mixtures and one diversity population were developed from winter wheat varieties and studied for physical, compositional and end-use quality traits for three years (2011–2013) under different European climatic and management conditions in order to study the stability of these traits resulted by the genetic diversity. The beneficial compositional and nutritional properties of the populations were assessed, while variation and stability of the traits were analysed statistically. No significant differences were found among the populations in low-input and organic management farming systems in the physical, compositional and processing properties, but there was a difference in the stability of these traits. Most of the populations showed higher stability than the control wheat variety, and populations developed earlier had higher stability than those developed later. Furthermore, some populations were found to be especially unstable for some traits at certain sites (mostly at Austrian, Swiss and UK organic sites). Protein content of the populations was high (13.0–14.7%) without significant difference among them, but there was significant variation in their gluten content (28–36%) and arabinoxylan content (14.6–20.3 mg/g). The most outstanding population for both protein and arabinoxylan content was a Hungarian cropping population named ELIT-CCP. It was concluded that the diversity found in the mixtures and CCPs have stabilizing effect on the quality parameters, but a higher stability was observed under low-input than under organic conditions. These results could be beneficial not only for breeders but also for the consumers in the long run.