With lifestyle changes, chronic diseases have become a public health problem worldwide, causing a huge burden on the global economy. Risk factors associated with chronic diseases mainly include abdominal obesity, insulin resistance, hypertension, dyslipidemia, elevated triglycerides, cancer, and other characteristics. Plant-sourced proteins have received more and more attention in the treatment and prevention of chronic diseases in recent years. Soybean is a low-cost, high-quality protein resource that contains 40% protein. Soybean peptides have been widely studied in the regulation of chronic diseases. In this review, the structure, function, absorption, and metabolism of soybean peptides are introduced briefly. The regulatory effects of soybean peptides on a few main chronic diseases were also reviewed, including obesity, diabetes mellitus, cardiovascular diseases (CVD), and cancer. We also addressed the shortcomings of functional research on soybean proteins and peptides in chronic diseases and the possible directions in the future.