Seed coat cracking and green seeds threaten soybean crop production. Seed coat cracking results from a complex interplay of genetic factors, environmental stresses, and crop management practices. Green seeds, linked to water deficit, nutritional deficiencies, and environmental stresses, exhibit reduced quality and viability. The intricate relationships between seed coat integrity and seed permeability, influenced by the lignin content, porosity, and color, play a pivotal role in seed germination, storage potential, and resistance to field stresses. These issues reverberate through the soybean agricultural supply chain. Strategic interventions are crucial to address these abnormalities and ensure soybean productivity. Seed germination and vigor are reduced due to seed coat cracking and green seeds, undermining food security and necessitating additional resources for disease management. The occurrence and identification of green seeds and seeds with cracks in the seed coat were also reported by identifying the genes and QTLs (quantitative trait loci) associated with these characteristics. Herbicides, commonly used in weed management, may offer a strategic approach to mitigating seed coat cracking and green seed occurrence. Understanding the complex interactions between the genetics, environmental factors, and management practices influencing seed abnormalities is essential as global climate change intensifies. This review emphasizes the need for integrated strategies, balanced plant nutrition, and cohesive phytosanitary management to mainly alleviate seed coat cracking and greenish occurrences in soybeans and other plant species.