Nutrient homeostasis is essential for plant growth and reproduction. Plants, therefore, have evolved tightly regulated mechanisms for the uptake, translocation, distribution, and storage of mineral nutrients. Considering that inorganic nutrient transport relies on membrane-based transporters and channels, vesicle trafficking, one of the fundamental cell biological processes, has become a hotspot of plant nutrition studies. In this review, we summarize recent advances in the study of how vesicle trafficking regulates nutrient homeostasis to contribute to the adaptation of plants to heterogeneous environments. We also discuss new perspectives on future studies, which may inspire researchers to investigate new approaches to improve the human diet and health by changing the nutrient quality of crops.