Integrated soil fertility management is a vital approach for sustainable linseed oil production in arid regions. To investigate the effect of different nutrient sources on biochemical indices and linseed yield under drought stress conditions, a split-plot experiment was conducted using a randomized complete block design with three replications. The study evaluated seven fertilization treatments including control, organic (Cattle manure, 30 tons per hectare), chemical (Nitrogen 100, phosphorus 40, and potassium 100 kg per hectare), and biological (Pseudomonas spp bacteria), along with integrated treatments of organic-chemical (30 tons cattle manure + 70% chemical), organic-biological (30 tons organic + biological), and chemical-biological (100% chemical + biological), under two irrigation regimes (normal and irrigation cutoff at flowering stage). Results demonstrated that drought stress reduced mean grain yield from 2000 to 1395 kg per hectare. However, integrated treatments, particularly organic-chemical and chemical-biological, mitigated the negative effects of stress by strengthening the plant’s antioxidant system. Under normal irrigation conditions, the organic-chemical treatment resulted in remarkable increases in dry matter (287%), proline (112%), and harvest index (52%) compared to the control. Ultimately, the implementation of integrated fertilization systems (Organic-chemical and chemical-biological) is recommended as the most effective agronomic strategy for improving quantitative and qualitative performance of linseed under water-limited conditions.