In this paper, the comparison was made between the content of oligosccharides, phytic acid, and trypsin inhibitors contained in protein preparations manufactured from bean seeds with the use of two methods: classical isolation and crystallization under acidic conditions. During the classical isolation process, proteins were reclaimed from alkaline extracts at a minimum solubility; they had an amorphous form (PBA). The second method consisted in the utilization of the ability of bean proteins to create crystalline structures at acidic conditions (PBK). The investigations performed showed that when the crystallization method was applied, it was possible to obtain preparations of lower contents of phytic acid and inhibitors compared to the classical isolation process. In the preparations obtained, the content of oligosaccharides was also decreased compared to the bean flour. The crystallization process caused a decrease in the content of galactosaccharides and their content was either at levels similar or lower than the respective levels of their content obtained using the classical isolation method. A thermal processing applied (100°C, t = 30 min) produced a decrease in the content of phytic acid, whereas the change in the contents of oligosaccharides and trypsin inhibitors depended upon the variety of seeds used.