Biofertilizers have become a viable substitute for chemical fertilizers. Biofertilizers contain the effective strains of potential organisms majorly included of bacterial and fungal strains providing desirable benefits to crop plants and soil. They are being prepared in different formulations suitable for diverse applications. Variations in production process, raw materials and storage conditions can lead to inconsistencies in microbial composition and nutrient levels, impacting their function in the fields. However, the shelf life and quality maintenance of biofertilizers are critical to their effectiveness and viability and present considerable hurdles throughout production, storage and application. Biofertilizers are easily affected by various factors resulting in eventual loss of viability. Variations in temperature, moisture content and exposure to UV radiation are a few examples of factors that might negatively impact microbial viability and activity. Furthermore, contamination by undesirable microorganism during production and storage can reduce the effectiveness of bio-fertilizers. To address these problems, innovative approaches such as different formulation techniques were developed. Addition of stabilizing agents to the formulation will add value to the products, since it gives protection to the cell, thus the efficacy and shelf life are maintained. Varied types of formulations have different issues with the maintenance of quality and shelf life. Widely used formulations and the problems and constrains with different formulations on application, in addition to shelf life and also the possible suggestions are discussed in this review.