This study evaluated the grain characteristics, dough rheology, and baking performance of two winter wheat cultivars, 'Edvins' and 'Fredis', grown in Estonia between 2021 and 2024. Seven fertilisation treatments were compared, including three organic (Org0, OrgI, and OrgII) and four conventional (N0, N50, N100, and N150), using data from a long-term crop rotation experiment. Yield, thousand kernel weight, protein content, wet gluten content, gluten index, dough rheology, and bread quality traits were assessed. Higher mineral nitrogen input in the conventional system enhanced both grain yield and quality traits, compared with the organic system, which yielded ~50% less. The N150 treatment yielded the highest loaf volume, achieving 575 cm³ from an initial input of 250 g of flour and exceeding Org0 substantially. Rheological traits were largely unaffected by the cropping system, except for dough development time, which was longer for flour from the conventional system. Cultivar 'Fredis' showed more stable quality across treatments. 'Fredis’ was associated with high yield and quality traits, while 'Edvins' was more sensitive to early-season climatic conditions. Cropping systems and nitrogen management are the primary drivers of winter wheat productivity and baking quality, while cultivar selection contributes to quality stability under organic production.