In agroforestry systems (AFS), where environmental conditions are highly variable at small spatial scales, the use of uniform genetic material of a single cultivar commonly grown in monoculture cropping might not be optimal. However, the use of composite cross populations (CCPs) that contain an inherent genetic variability might be a promising approach under the environmental variability created by trees in AFS. In this experimental trial, the performance of a CCP (‘CC-2 k’) of winter wheat was compared to a commercial variety (‘Wiwa’) in a split-plot design at two AFS (Feusisberg and Wollerau) in Central Switzerland. Yield of CC-2k (1.9 ± 0.7 Mg ha−1) was higher than yield of Wiwa (0.7 ± 0.4 Mg ha−1) in Wollerau, but yields did not differ between CCP and variety in Feusisberg (1.9 ± 0.7 Mg ha−1 and 2.0 ± 0.8 Mg ha−1, respectively). The interaction of site and variety was significant (p < 0.05). Wiwa had a higher protein, Fe and Ca content than CC-2k. Therefore, while the CC-2k outperformed Wiwa in terms of yield in one of the two AFS, Wiwa outperformed CC-2k in terms of quality. In this one-year field experiment, the composite cross population might have been better adapted to the heterogenous environment of agroforestry systems (found in one out of two sites) but failed to reach the high-quality product of modern cultivars. These initial results must be seen as first insights which need to be complemented by larger field experiments for generalisation. The findings of this study may be interpreted as an indication that further improvements in terms of quality might make CCPs a viable option for diversified agricultural systems with larger environmental heterogeneity than common monoculture cropping systems.