This review systematically analyzes the mechanisms through which fungi affect key physiological processes in plant organisms. Plant–fungus interactions play roles in photosynthesis, nutrient acquisition, hormonal regulation, and stress adaptation, both in pathogenic and symbiotic contexts. Negative effects induced by pathogenic fungi are associated with tissue destruction, disruption of water and mineral balance, mycotoxin production, and increased oxidative stress. In particular, species belonging to the genera Alternaria, Fusarium, Phytophthora, and Aspergillus affect photosystem II activity, damage chloroplast structures, and promote the accumulation of reactive oxygen species, resulting in reduced photosynthetic productivity, which represents a central pathophysiological mechanism. At the same time, the positive functional roles of fungi are indispensable. Arbuscular mycorrhizal fungi have been shown to enhance nutrient uptake, increase photosynthetic rates, and improve plant tolerance to abiotic stresses such as drought and salinity, as reported in numerous studies. The participation of saprotrophic and symbiotic fungi in carbon and nitrogen cycling, stabilization of organic matter in soils, and bioremediation processes is recognized as a key factor for ecosystem sustainability. The sink effect generated by fungi is described as an important ecological mechanism that promotes the sequestration of carbon in soils. In conclusion, a comprehensive understanding of plant–fungus interactions provides a scientific basis for optimizing agricultural systems, maintaining soil health, and promoting sustainable ecosystem management.