Compost and biological ameliorants fertilizer may improve growth and productivity of stressed-crops. However, these improvements on the soil and crop performance under alkaline-salt stress have not yet been fully understood, particularly in arid regions. The study aimed to assess the influence of geranium straw compost (GSC) and effective microorganisms (EMs) under saline calcareous soil on soil physicochemical status, morpho-physiological responses, antioxidant capacity, ionic homeostasis and dry matter of chia. Nine treatments across two variables were studied using a randomized complete block design in three replications in 2023-24 and 2024-25 seasons. GSC levels, with 10, 20 t ha(- 1), were added to saline calcareous soil (ECe = 7.79 dS m(- 1) and CaCO3 = 15.32%), in addition to non-added one (as a control). EMs treatments were applied on the foliage at concentration of 1% and 2%, in addition to control (distilled water sprayed). Compared to the corresponding control, GSC or EMs considerably improved chia's growth and dry mass production, leaf pigments, chlorophyll fluorescence and photosystem II efficiency, osmo-protectant constituents, enzymatic and non-enzymatic oxidative metabolism and leaf nutrients efficiency, respectively. In this sense, integrating soil additions with 10 or 20 t GSC ha(- 1), along with 2% EMs noticeably attenuated the negative impacts of salt stress via restoring growth and biochemical responses, stimulating antioxidant defense system, and maintaining ionic homeostasis, resulting in high-produced biomass by 252.1% or 407.6%, respectively. All of these could be linked to the beneficial impacts of GSC on soil properties, which have been improving root function by lowering ECe, pH, and BD while boosting TP, CEC, and water retention or nutrient-cycling properties. Furthermore, EMs suppressed MDA-induced lipid oxidative stress (lowered by 69.6% or 72.0%, respectively), equilibrated ionic scale, and catalyzed RuBisCO enzymes that support net photos-assimilates and govern the biomass partitioning. Conclusively, findings recommended adding 20 t GSC ha(- 1) for amending saline calcareous soil and feed the chia foliage with 2% EMs to reduce the impact of salt stress and improve biomass production under aridity conditions.