The stigmas of saffron (Crocus sativus L.) are known as “red gold” for being the most expensive spice of the world. This medicinal crop grows well in the regions with cold winter Mediterranean climate. However, salinity can be one of the limiting factors for its cultivation in these regions. Composted manures and their co-compost with wood-derived biochar as fertilizers in saline soil can reduce the salinity stress on saffron. In this study, the composted manures from dairy farms (FYM), sheep and goats (SG) and poultry (PM) and their co-compost with wood-derived biochar (FYM-B, SG-B and PM-B) were amended in non-saline (EC1:2 0.25 dS m−1, SOM; 9.9 g kg−1) and soil with natural slight salinity (EC1:2; 1.95 dS m−1, SOM; 30.9 g kg−1) soil for two consecutive years with the total amendment rate of 65 t ha−1 for each fertilizer. The saline soil was transported from an agricultural farm (30 km away from research field); whereas, the non-saline soil was not transported and was not cultivated before. The amendment of fertilizers and sowing of corms were conducted at the same time in the mid of August. The stigma yield in saline control soil was significantly lower than non-saline control in both cropping years. In non-saline soil, all fertilizers reduced stigma yield of first-year crop by 14–60 % (P < 0.05). No differences between treatments for the stigma yield of second year crop in non-saline and of first year crop in saline soil were observed. In saline soil, FYM and PM fertilizers increased stigma yield of second year crop by 44 % and 41 %, respectively (P < 0.05). The two-year cumulative agronomic efficiencies for nitrogen and phosphorus and the nitrogen use efficiency for leaf biomass were lower under fertilizer treatments than control in non-saline and saline soil. In non-saline soil the PM-B; whereas, in saline soil all fertilizers (except SG) increased the phosphorus use efficiency of leaves (P < 0.05). The two-year amendment of composted manures and FYM-B in non-saline soil resulted in high uptake of sodium in leaves (P < 0.05); whereas, such effect was not observed for saline soil. Almost all fertilizers increased ∼2–5 fold the concentration of bioavailable phosphorus and ∼2–3 fold the concentration of potassium in non-saline and saline soil (P < 0.05). The positive influence of fertilizers on stigma yield and PUE of leaves of second year crop was observed only for saline soil. Furthermore, contrary to the results for non-saline soil, these fertilizers did not cause an increased uptake of Na in leaves in saline soil. We attribute this effect to the high concentration of SOM and gradual decline in EC (0.94–1.71 dS m−1) over time in saline soil. The gradual improvement in yield (from negative to neutral in non-saline and from neutral to positive in saline soil) was observed over time. Amendment of fertilizers and sowing of corms at same time may be the reason for their negative influence on stigma yield in low SOM-containing non-saline soil.