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The application of biofertilizers in pulse crop agriculture has garnered significant attention as an eco-friendly and sustainable alternative to conventional chemical fertilizers. This comprehensive review aims to elucidate the progression of biofertilizer technologies from traditional single-strain inoculants to contemporary microbiome-based strategies. Pulse crops, such as beans, lentils, chickpeas, and peas, are pivotal in global agriculture due to their high protein content, nitrogen-fixing ability, and role in improving soil health. However, optimizing their productivity necessitates effective nutrient management, where biofertilizers play a crucial role. Initially, biofertilizer development concentrated on single-strain inoculants, predominantly Rhizobium species, which establish symbiotic relationships with leguminous plants to enhance nitrogen fixation and improve crop yields. Despite their proven benefits, single-strain inoculants often exhibit variable performance influenced by soil conditions, climatic factors, and interactions with indigenous soil microbiota. This variability highlights the need for more consistent and resilient biofertilizer solutions. Recent advances in microbiome research have paved the way for the development of microbiome-based biofertilizers. These advanced formulations leverage the synergistic interactions among diverse microbial communities, including bacteria, fungi, and archaea, to provide a more comprehensive and stable enhancement of soil fertility and plant growth. Microbiome-based approaches recognize the complexity of plant-microbe-soil interactions, offering improved nutrient cycling, increased plant stress resilience, and better adaptation to various environmental conditions. The benefits of microbiome-based biofertilizers are manifold, encompassing enhanced nutrient availability, improved plant health, and sustainable soil management. However, their development and application pose several challenges, including understanding the intricate dynamics of microbiome interactions, developing precise formulation and application methods, and navigating regulatory landscapes. Addressing these challenges requires multidisciplinary research and innovation, integrating genomics, metagenomics, and advanced data analytics to unravel the complexities of soil microbiomes. This includes the potential for personalized biofertilizer formulations tailored to specific soil and crop conditions, enhancing the efficacy and scalability of biofertilizer technologies.