Baking quality of organic winter wheat remains a significant challenge, primarily due to the usually lower grain protein concentration realized in organic agriculture. This study examined eighty-four winter wheat genotypes from Europe under organic conditions in the south-east of Romania, during two contrasting seasons. Various quality traits, i.e., grain protein content, bread volume, dough strength, breakdown and extensibility were analyzed. All examined traits exhibited significant differences among cultivars. Molecular assays, utilizing markers for Glu-A1, Glu-D1, Glu-B3g and NAM-A1 loci revealed genetic diversity within the germplasm. The study highlighted sixteen genotypes with bread volume statistically significant different from the average trial. In the organic system the Glu-A1x2* allele had positive effects on bread volume, water absorption, dough strength and extensibility. At Glu-D1, the alleles for Dx5 + Dy10 were detected in over 85% cultivars and showed positive effects on dough development time and extensibility. Another locus with positive effect on baking quality was NAM-A1. In this study the haplotype NAM-A1c had the highest frequency (51%), followed by NAM-A1d (38%) and NAM-A1a (11%). Both NAM-A1a and NAM-A1c haplotypes positively affected bread volume, water absorption, dough strength and extensibility. The Glu-B3g allele had a positive effect on development time. However, these genes could not explain the whole variation of quality parameters, as some of the best cultivars had unfavorable alleles while other cultivars carrying positive alleles had low quality. Obviously, other factors strongly influenced the quality parameters in organic agriculture, and further research is needed to understand their nature. Our results suggest the potential for achieving improved breadmaking quality, under organic conditions, by exploring genetic possibilities. However, combining suitable breadmaking quality with high yield will remain a challenge.