The quality of flour is influenced by various factors including genotype, environmental and agronomic conditions, post-harvest grain storage, and milling technology. Currently, the EU focuses on reducing mineral fertilization and promoting less intensive agrotechnology (organic and integrated farming). This research aimed to assess the baking value of flour obtained from four spring wheat cultivars cultivated in three farming systems: organic (ORG), integrated (INT), and conventional (CONV). The wheat grains were sourced from a three-year field experiment (2019–2021) conducted at IUNG-PIB in Pulawy, Poland. Results indicate that the CONV generally yielded more favourable qualitative parameters for the flour, including significantly higher protein content, wet gluten, falling number, and farinographic characteristics such as dough development, stability time, and quality number. Nevertheless, most flours from the ORG system met the quality requirements for the baking industry, showing adequate protein content, wet gluten, and falling number. However, flours from the INT system stood out due to significantly higher water absorption, resulting in increased dough and bread yield. Additionally, bread baked from these flours exhibited a significantly higher bread volume. In sensory evaluation, bread from CONV flours received the highest scores, although the differences in the overall acceptability were not significant.