The long-term use of chemical fertilizers poses a serious threat to crop productivity and soil quality. Organic fertilizers are used to improve the soil fertility and crop productivity. The application of organic fertilizers improves soil health and plant growth by improving the soil organic matter (SOM), soil structure, aggregate stability, nutrient uptake, water-holding capacity, cation exchange capacity, nutrient use efficiency and microbial activities of soil. The intensity of abiotic stress is continuously increasing, which is a serious threat to crop productivity and global food security. However, organic fertilizers have been reported to improve tolerance against drought, salinity, heat and heavy metal (HM) stresses. The application of organic fertilizer improves the leaf water status, nutrient uptake, nutrient homeostasis, synthesis of chlorophyll, osmolytes, hormones, secondary metabolites, antioxidant activities and gene expression, resulting in improved tolerance against drought, salinity, heat, and heavy metals. In the present review, we have discussed the ability of organic fertilizers to improve soil fertility, crop yield, and the nutrient use efficiency. We have also presented the various mechanisms through which organic fertilizers improve tolerance against drought, salinity, heat, and heavy metals. Therefore, this review will put forth new directions for researchers working on the use of organic materials to improve soil fertility, crop productivity and tolerance against abiotic stresses.