Current soil management methods rely heavily on inorganic chemical-based fertilizers, posing a significant health and environmental risk. Because of their potential significance in food safety and sustainable crop production, the use of beneficial microorganisms as a biofertilizer has become more important in the agricultural industry. Plant growth promoting rhizobacteria (PGPRs), endo- and ectomycorrhizal fungi, cyanobacteria, and many other beneficial microscopic organisms were used in a variety of ways to enhance nutrient absorption, plant growth, and plant tolerance to abiotic and biotic stress. The current review focused on the role of biofertilizers in crop functional traits such as plant growth and productivity, nutrient profile, plant defense and protection, with a particular focus on their ability to trigger various growth- and defense-related genes in the signaling network of cellular pathways, resulting in cellular response and, as a result, crop improvement. The information acquired from the literature reviewed here will aid us in better understanding the physiological underpinnings of biofertilizers, which will aid in the development of sustainable agriculture by minimizing the issues connected with chemical fertilizer usage.