Linseed is an important industrial crop cultivated for its edible seeds and fiber linen. Organic fertilizers have beneficial effects on soil properties and quality of crops. Therefore, we conducted two field experiments during 2018–2019 and 2019–2020 to determine the effect of organic fertilizers on soil fertility, yield and fiber quality of linseed varieties Roshni, BL1 and Chandni under low soil moisture conditions. We prepared organic fertilizers from seed cake of Eruca sativa, leaves of Moringa oleifera and chicken peat in various combinations by composting method. The various formulations of organic fertilizers included OF1(1 kg seed cake of Eruca sativa), OF2 (1 kg seed cake of Eruca sativa + 1 kg chicken peat), OF3 (1 kg seed cake of Eruca sativa + 0.5 kg chicken peat + 0.25 kg Moringa oliefera leaves) and OF4 (1 kg seed cake of Eruca sativa + 0.250 kg chicken peat + 0.5 kg Moringa oliefera leaves). Compositional analysis of organic fertilizers indicated that OF3 and OF4 had higher and may potentially sufficient quantities of NPK and organic matter. Both of these fertilizers significantly improved soil total N, available P, K, Zn and Fe contents. Growth response of linseed varieties to organic fertilizers was evaluated under water deficit stress (40% field capacity of soil) at tillering stage for one month. Water stress had significantly adverse effects on plant height, production of tillers per plant, leaf relative water content (LRWC), number of capsules per plant, thousand seed weight, total seed yield, straw yield, fiber length and fiber weight of linseed varieties. However, the application of OF3 and OF4 significantly enhanced plant height, tillers production, LRWC, seed yield, straw yield, fiber length and fiber weight under water deficit stress. Water deficit stress also resulted in a significant increase in the content of phenolics of both the leaves and roots. For each measured quality parameter of linseed varieties, organic fertilizer treatments resulted in higher values than untreated and irrigated control. We concluded that organic fertilizers particularly OF3 and OF4 significantly improved soil fertility and minimized negative effect of water deficit stress on plant height, tillers production, LRWC, seed yield, straw yield, fiber length and fiber weight of linseed varieties.