Owing to concerns about animal proteins, resource limitations, and population growth, there is growing interest in exploring soybeans as animal protein alternatives to fulfill consumption requirements. Black soybean (BS) has superior nutritional and health benefits, compared to yellow soybean (YS). However, BS has been explored less often than YS. While previous reviews have individually focused on the nutritional composition, bioactive compounds, or health benefits of BS, they have not delved into the intricate mechanisms underlying these interactions, especially the distinct roles of the individual components. This comprehensive review aims to bridge this gap by providing an overview of the key nutritional composition and bioactive compounds in BS associated with health benefits, as well as the possible mechanisms underlying these changes. Various processing technologies (physical, biological, and thermal) have been applied to BS. Additionally, the bioavailability, biotransformation, and safety concerns of BS were studied, as these factors are crucial for its potential application, such as natto, films, and microcapsules. However, there are some gaps in the application of BS and YS. In the future, it will be worth exploring the effects of BS protein as meat analogs, 3D printing constituents, and amyloid fibrils, as well as BS lipids as oleogels and BS seed coats as bioactive ingredients in pharmaceutical products.